The Saiyans: By the time they're in their twenties, they still look like teens or preteens, and it isn't until well later on in the series that they're looking like adults (though Vegeta goes through this relatively quickly). Even to the degree that in Dragon Ball GT/Late Dragon Ball Z it gets highlighted by Vegeta, saying that he might be in his 50s, but he ages slower than the rest of the cast. Bulma does not enjoy this.
Vegeta's brother Tarble is probably the best example of this as far as Saiyans go- he looks like he could be in his teens despite being older than Goku, who was around 40-years-old when they met.
In the original Dragon Ball Goku looks around seven when he's twelve, and at age fifteen he looks more-or-less the same. It's not until age eighteen that he finally starts to look like a teenager.
Mrs. Briefs, Bulma's mother, doesn't seem to get any older over the entire course of the series. By the Buu Saga, her daughter is over 40, and she looks the same as she did when she'd first appeared roughly 25 years earlier.
Bulma also qualifies in the Buu Saga. At that point she's in her early 40s, but could still easily pass for late 20s/early 30s.
And then there's Chiaotzu, who looks like a 10-year old child through his entire life. By his last appearance in Z, he's 46-years-old, just one year younger than Goku, and he still looks like a little kid. This is kind of explained in that his original design was based on a traditional Chinese ghost.
A non-human/Saiyan example might be Frieza. Between flashbacks to the Bardock Special, which occurred at least twenty+ years ago, to the present, he hasn't visibly aged a bit. He could easily be Really 700 Years Old, but his age is never given.
Krillin, who has incredibly low height, does not look his age throughout Dragon Ball Z.
In Part II, Joseph's brain nearly breaks trying to comprehend how Lisa Lisa could be fifty years old. The answer, incidentally, is the Ripple. Supernatural powers in this series slow aging.
In part IV, Koichi Hirose starts out at 16 years old, but one could easily mistake him for an elementary schooler due to his short height and his Cross-Dressing Voices
Faye Valentine from Cowboy Bebop is much older than she appears, having been cryogenically frozen for 54 years while recovering from injuries she sustained on a space shuttle accident (possibly one of the first public space shuttles).
Saito Hiraga from Zero no Tsukaima. He looks no more than 13, but is in fact a 17-year old.
Even worse is his Tsundere mistress, Louise, who only looks ten at the most and is the same age as Saito.
Libra Dhoko from Saint Seiya fills both this and the Younger than They Look trope (oddly enough). He's over 200 years old, with a body of a 21-year old (after shedding his old skin) OR a 21-year old in a very old body.
Mika-sensei in Doki Doki School Hours is a 27-year old woman, though she appears to be ten years old. This doesn't prevent one of her students, Kitagawa, from being attracted to her. In fact, it encourages it.
Ymir is an unusual example. She was trapped in Titan form for 60 years, and did not age a single day during that time. As such, she is technically in her late 70s but looks to be in her late teens.
In Please Teacher!, Kei is a 18-year old male lead who is functionally fifteen years old due to a coma that resembled suspended animation. Among other things, this also served as Lampshade Hanging to explain the contrivance of him and Mizuho shacking up together, since eighteen is minimum age to marry... And in a plot twist late in the story, he finds out that the Little Miss Snarker in his circle of friends has the exact same condition, and is actually in her twenties.
Minnie-May Hopkins from Gunsmith Cats took "growth retarding" drugs in order to appeal to a certain type of clientele in a brothel. However, this is supposed to be squicky to the viewers. It squicked out the American editors so much they reversed it in their translation so she's taking drugs to counter an unnamed medical condition.
In the English version, May had tried to make herself look older than she was in childhood in order to not squick her adult boyfriend so much (he was Lolicon, but understandably had serious issues about the morality of their relationship) but it backfired, leaving her first looking older than she was, but not growing an inch since.
Somewhat related cross-cultural example: when Digimon Tamers was translated for Western network television, they raised the kids' official ages by a few years (from ten to thirteen), possibly due to what happens to them and the relations they get into squicking the translators a bit. Digimon Adventure 02 and Digimon Frontier also had all the kids ages raised a year.
The same thing happened with 4Kids' version of Tokyo Mew Mew, presumably for similar reasons; an especially jarring example is Bu-Ling, who begins the series at eight years old, yet the dubbed version managed to make her fourteen. Oddly, Tokyo Pop's manga translation moved the characters down a year to appeal more to a young audience.
The main character of Shibatora is a 22 year old police detective, but is frequently mistaken for a middle school student.
This is more Koge-Donbo's style than anything else. In one panel in the first chapter, Karin is shown drawn as her true age; for almost all of the rest of the series, she and her classmates are drawn as chibis. The same goes for the author's other series Pita-Ten.
Hagu from Honey and Clover is apparently 18 at the begining of the series, despite looking and acting like an 8-year old — which doesn't keep some guys from falling in love with her.
Which is made worse by the fact that it is openly stated she stopped growing at six and she barely changes by the time she's twenty.
Galaxy Angel has Mint, a 15-year old who looks like she's ten.
Subverted in Mai-HiME (which does in fact include a character fitting this trope, just not that one):
Natsuki: How old do you think I am? Mai:(confused) Aren't you a high school girl? Natsuki:(annoyed) That's not what I meant. I'm seventeen. I was away from school for a year.
Presumably the first Club President of Genshiken, who later turns out to have been the only Club President the Society for the Study of Modern Visual Culture had ever had until he handed it off to Madarame. The members briefly speculated how old the Prez actually was after finding manga books in the clubroom that date back to 1987.
Done in Suzumiya Haruhi with Mikuru Asahina, who is described in the series as "Lolita-looking". She's seventeen, while the rest of the cast is sixteen. She also happens to be Ms. Fanservice and have Gag Boobs, yet still manages this title.
Then there's the whole Time Travel thing (and her playful refusal to answer any of the Genre Savvy Kyon's inquiries about the matter), which makes her real age pretty much impossible to determine. Given the possibilities of future medicine, she could be in her thirties for all we know.
In Welcome to the NHK, one of Satou's "study materials" (i.e. eroge) has a cover with a big-eyed, small-chested girl... and the title of the game is actually "I Am Not Loli!"
There's a rather odd version of this in Zettai Karen Children where the Evil Mentor who looks like a middle school student is really in his 80s. This changes his stated intent to "groom" the titular 10-year olds from weird to squicky.
Let's not forget also the said evil mentor's childhood friend and Good Counterpart, three years older Fujiko, who looks and behaves like a horny teenage Kawaiiko, but notwithstanding her looks the titular "children" characters often call her "granny".
In the Eureka Seven manga, Matthieu tells Renton that "the thing about Eureka is... she may not look it, but she's actually 30!" much to Renton's shock. This is revealed to be a lie simply to get Renton's goat the very next panel.
In Eureka Seven Ao, Eureka is a good deal older than she was in the original series (it's more complicated than that due to time travel hijinks), but still looks roughly the same as she did in the past (mostly because she isn't human). She does pull off an older look, though, by way of clothing choices and hair styles.
Asuna Kagurazaka of Mahou Sensei Negima!, who looks and is assumed by the people around her to be 14. It isn't clear just how old she is, but flashback chapters later in the manga have confirmed her to have traveled as a little girl with Nagi's company — twenty years ago (it turns out she's over 100 years old). It should be noted that Takamichi, Asuna's adult teacher who also traveled with Nagi, was also a little kid at the same time.
It's hinted that Takamichi spent a lot of time training in Evangeline's time condenser, and therefore his actual age may not match his chronological age.
Also, Fate Averruncus and Zect Filius, the two white-haired pretty boys: While Fate apparently bathed in some Fountain of Youth, Zect is referenced as a "man" despite looking way younger than "Just a little brat" Nagi. And nobody finds this weird, so it may be a racial trait or something.
Then we've got the normal (we think) girls like the Narutaki twins, who look ten years old despite being around fifteen like the rest of the class. They're actually the oldest, other than the vampire and ghost. Likewise, the oldest-looking girl (Chizuru) is actually the youngest.
Major Kusanagi in Ghost in the Shell is age 44 at the time she meets the Puppet Master/the Pupetter and a few years younger in Stand Alone Complex, but her almost completely artificial body looks noticeably younger.
And in one episode there's a female Russian assassin with a similar cybernetic body, who is said to be over 80.
All the demons in Chrono Crusade fall under this, but Chrono in particular. Thanks to a need to conserve his spiritual energy, his typical form makes him look like twelve years old, and even in his true form he looks like he's in his early twenties. However, there's at least about 60 years that he's confirmed to have lived, and it's likely he's much, much older. His former comrades, the sinners, all appear to be in their late teens or early twenties, but they're all near the same age.
There's also Father Remington (who appears to be in his early thirties at the latest but is seen dueling Chrono half a century prior in a flashback).
In the manga finale Fiore/Floretta and Satella (due to becoming Human Popsicles for 75 years).
The extreme cases fell on Konata, Kanata and Yutaka — their heights are 1.42 m, 1.43 m and 1.38 m respectivelynote For those of you less familiar with metric, that's 4'8", 4'8Ľ", and 4'6" respectively. The relation between this trope and Lolicon has been thoroughly explored: Kanata is the (deceased) wife of Soujiro, and Konata wore School Swimsuit to attract "people with special interests" in the Beach Episode, and when Yutaka lamented her lack of boyfriend due to being an illfauxli, Konata told her that a lot of people are looking for her, should she not choose...
Cinque looks like she's around ten, but she's one of the oldest members of the Numbers Cyborgs, and is officially the same age as Teana.
Fate's familiar, Arf, in the third season when a ten year Time Skip means she actually is old enough to appear as a grown woman... and she looks like a child in order to conserve energy. Before that, she was Younger than They Look.
And in a less extreme example (also from the first two seasons), Chrono Harlaown looks to be roughly nine or ten years old, just like Nanoha, Yuuno, Fate, etc. In reality, he's fourteen.
Lutecia: Even though we've got one shrimp, the three of us are of the same age. Caro: What did you say!? But I've grown taller by 1.5cm!
Precia Testarossa, the Big Bad of the original series, looks like she's in her 20s. She's 54.
Likewise, by the time of StrikerS, the now 41-year-old Lindy Harlaown doesn't appear to have aged a day in the 10 years since her first appearance. And for that matter, in the original series she was 31 and looked like she was in her early 20s.
Also L, who can blend in with a group of teenagers in his mid 20's.
Many don't realize that Misa is older than Light. The folks at Viz Media even make this mistake in one of the DVD commentaries. Justified in that her young looks are accompanied by extremely childish behavior.
Tsubasa Shibahime from Kare Kano is a high schooler like the rest of the cast, but looks like she's twelve.
Mitsukuni Haninozuka from Ouran High School Host Club looks and acts like a 10-year old to appeal to the Shotacon crowd, but is really 17/18 years old, and therefore, the oldest member of the club.
The joke is that his birthday is February 29th, which comes around only once every 4 years. Since this is manga/anime, he only ages 1 year for every 4. Also, going by that logic, wouldn't the same go for his chronological age and he be 5?
Thorkell from Vinland Saga is a more realistic example than most but he still in no way looks like he's in his fifties.
Azuma and Seira Umeda from the manga series Hana-Kimi. They both look pretty young despite the fact that Seira is fifty-one and Azuma is fifty-four.
The art style of Hidamari Sketch made everyone like this, but Yuno needs some specific mention. Her extreme proneness to childlike mood swings/general childish behavior and her 1.44m height made her seem more like seven than fifteen. Actually part of this series' premise was on her trying to grow out of this.
A Certain Magical Index: Komoe-sensei looks very young (no older than ten) and wears bunny pajamas to bed. Yet she is an adult, and her apartment is littered with beer cans and cigarettes. Quite a contrast there. For the longest time, there was no explanation for this, but in later volumes rumors eventually surface that she was the subject of some kind of age-regression experiment.
Yun-Ook Jang, the main character in Forest of Gray City is a 25-year old who keeps getting mistaken for a teenager.
The manga Double Arts pulled this on one of the main characters. She goes to meet a new found friend's family, and is introduced to a little girl she assumes to be his little sister. But wait! That's his mom!
A very similar situation to the one above happens in the manga Code:Breaker, although this time with the female protagonist's mom, and the mom being a bit more endowed.
Rurouni Kenshin: Kaoru refuses to believe that the youthful-looking Kenshin is a whopping 28 years old, although that doesn't stop them from getting together in the end—even though Kaoru is only 17. Likewise, when Yahiko and Misao discover that Hiko is a remarkably well-preserved 43, they wonder if it's a side-effect of the Hiten Mitsurugi style.
And speaking of Misao, she's 16, but looks quite a bit younger, something that she doesn't react well to. One particular filler episode had all the female characters poke fun at this, even innocent little Tsubame, who is shocked that Misao is that much older than her.
Hinako Ninomiya, from the series Ranma ˝. She has the appearance of an innocent child though she is actually much older. When she drains the battle auras of "delinquents", she reverts to her true age and becomes a buxom woman in her late twenties.
Also Lukkosai, from the Ranma ˝ manga, who is the same age as Happosai but is cursed to turn into a little boy when splashed with cold water.
The manga Cardcaptor Sakura's Eriol Hiiragizawa is actually the same age as Sakura's father, despite looking to be around the same age as her because he magically halted his aging process.
Tsubasa Reservoir Chronicle: Syaoran is subjectively around 21 when the series begins (Time Travel is involved). He looks like a young teenager. The clones don't look any older than he is at the end, but both of them are in their early-to-mid 30's... yes, the clones are older than their originals. It's complicated.
Fai looks to be in his twenties, but isn't. His real age is never said, but Yuko commented that despite his apparent youth he had already lived several lifespans.
xxxHOLiC: Watanuki takes over Yuuko's shop after her death, he goes into a similar un-aging and anomaly-to-the-universe state. By the end of the series he's over 100 years old but physically looks barely older than the teenager he was when the series started.
Angelic Layer's Misaki Suzuhara is of 1st year middle school age. Yet she gets mistaken for much younger, at one point elementary 3rd year, much to her shock.
A similar thing happened in Magic Knight Rayearth, another CLAMP series: after Hikaru stated that she was fourteen years old, Umi and Fuu were shocked (Hikaru was shorter than the other two by at least a foot), and one of them said that she thought Hikaru was still in elementary school.
An element of Cephiro is people being able to change how old they look. Character bios for the childlike Clef and Emeraude state that they are Really 700 Years Old. This is averted in Rayearth OVA.
God from Maria†Holic came upon a long rotted love letter given to her years before, which looked to be pre-War Japan. She looks no different than she does in the present, and since she looks to have been the dorm leader even then, she would have to be at least 70 or 80. Also, Yonakuni.
In Mahoromatic Suguru's teacher is shown to look exactly the same at the series end as at its start; the series ended after a twenty year Time Skip where she considered Suguru too old at the ripe age of thirty four. This kinda begs the question; how old was she at the series start?
Two of the Sannin in Naruto have this; Tsunade uses a transformation jutsu to keep herself looking like she's in her late twenties or early thirties (however, the use of her other jutsu makes her appearance without it appear even older than she really is). Orochimaru's body-switching jutsu causes him too look like he's still in his early-to-mid-thirties. Both are between 50 and 53 years old. Jiraiya presumably doesn't use any jutsu to keep himself looking young, as he is the only one who looks his age.
There's no reason a 50-something man can't have a toned body.
In the third movie, Sakura fights a female assassin named Karenbana who appears to be about 12. When Sakura says to her, "You wear too much perfume for a kid", she replies with, "Kid? I'm twenty-two!" to which Sakura replies, "Oops!"
Sasori is 35 years old. But because he modified his body to become an unaging puppet, his physical appearance is that of a 15-year old.
The First Hokage lived long enough to have grandchildren. Nevertheless, neither him nor his brother the Second Hokage look like they've aged beyond their early 40s; for all we know, they could have been relatively young when the grandkids were born.
When they meet, Naruto instantly assumes that Yagura is a child who never had the chance to properly experience life. He's actually both an adult (though his age isn't given) and the Fourth Mizukage to boot.
Alicia from ARIA is 19 years old and pretty much looks that way, which doesn't match well with her supposed long experience as an undine. She lives on Mars though, where the years last almost twice as long as earth's. Do the math.
President Aria from ARIA. 20 years have passed and he doesn't look any different, unlike Grandma, who has considerably shortened.
Played even straighter by Albert Pitt, who, while one of the eldest members of the main cast, looks like a cute little boy due to his working conditions.
Loco from MÄR is thirty-two years old, despite looking like she's somewhere around ten. This is because the Darkness Arms she specializes in de-age her every time she uses them. At one point she ends up de-aging herself into infancy.
In Black Cat, because of being shot with a nanomachine Lucifer bullet, Train transformed into a kid (that looks around 7-8 years old), even though he's actually 23.
Ranewater Calder from Zombie Powder, leader of the Ash Daughter Gang. Although he looks like a young boy, is actually an old man who manages to retain his youthful looks with Phoenix-Samin. His nickname is actually "Old Man Calder".
Mikako Koda from Paradise Kiss is around fifteen years older than her sister Miwako, and they both look like twins.
In the anime of Venus Versus Virus, twins Lola and Layla don't look much older than ten, but they're actually much older than Lucia and Sumire, the main characters, as they're ageless dolls.
In the original manga, they're just normal (human) girls.
Break and Sharon from Pandora Hearts don't age and are at least ten years older than they appear. Break is around 120 years old, though he looks like he's in his twenties. Sharon looks 13, but is really 23. There's also Zwei. Another example is Rufus Barma, who appears to be in his twenties or thirties despite actually being over seventy years old.
Given the bizarre way that time works in the Abyss and that most of the characters are contractors, most of the cast actually falls into this. Apart from the above examples, there's Oz, who is 25 though he still looks 15, and Vincent and Gil, who look in their early twenties, were eight and nine years old at the Tragedy of Sablier... a hundred years ago. The Baskervilles also apply as they have been seen in flashbacks over one hundred years ago.And Alice, for that matter. Interestingly, when the lack of aging from first brought up, Break had said that it was a 'possible' side-affect from entering in a contract. So far every contracter has been proven to be older than they look, it makes you wonder why they bothered adding in the 'possibly'.
Now in all likelyhood this applies to Riem also due to his contract witht the March Hare.
In School Rumble, Yakumo is calm, mature, and the object of Hanai's affection. Tenma is short, acts childish, and has Expressive Hair. Try and guess which one is older.
Seguchi Tohma owns this trope. He's 32 but looks 16. In the flashbacks where he's supposed to be 16, he looks twelve. Same problem appears with a bunch of other characters in Gravitation as well.
Yugi's childlike appearance is a source of comic relief in both the Yu-Gi-Oh! manga and the first series. He's supposed to be sixteen years old. He looks about ten. It's played with even more when you consider his child-like innocence, and how physically vulnerable he is compared to everyone else in the cast. It also bugs him a lot when people mistake him for a grade-schooler.
Yuuki of Saki. First year high school student who plays the role of Token Mini-Moe since she still looks like a kid. Koromo is even worse, she's manages to look even younger than Yuuki despite being one year older, to the point at which a security guard mistakes her for a little kid, rather than a high school mahjong player. In fact, Koromo's the oldest member of the Ryuumonbuchi team, albeit by a small margin, since they're all second-years.
Similar to Koromo, Kurumi of Miyamori is quite short and is occasionally childish, but she is, like her teammates (which includes the incredibly tallToyone), a third-year in high school.
Hayari Mizuhara, a pro player, is 28, something that is repeatedly pointed out every time her name is shown, despite (or because) of how she has a youthful-looking face that hasn't changed much since she was 11.
In NEEDLESS, Disc is a half-cyborg from the time before the big war. This makes her over 100 years old, despite her appearance as the Token Mini-Moe. When this is pointed out in episode 7, Adam is less than pleased.
The age of Road from D.Gray-Man is revealed in chapter 187 to be over 35. What isn't known is whether the young form we see is her real body, or an illusion; for example, although we know she is human, we've also seen her in the form of a doll.
Shown in chapter 215 to be true of Allen as well. The Fourteenth is shown wondering why Allen's body hadn't aged in the last 35 years.
Yellow from Pokémon Special. All the Johto Dex Holders have a hard time believing that someone a foot shorter than them is in fact a year older.
Magical Pokemon Journey has Ginger, who introduces herself as Coconut's sister. She appears to be around 16, which makes her overtones with Grandpa really really creepy...until Coconut reveals that Ginger is her GRANDMOTHER, and Grandpa's wife. Apparently she'd discovered a youth formula.
Momiji from Fruits Basket looks and acts like an elementary school kid. When Tohru finds out that he's going to go to her high school, she is shocked.
He eventually goes through a growth spurt, and becomes as Bishōnen as the rest of the boys (if not more).
Souichi Tomoe, Hotaru's dad in Sailor Moon, is in his late thirties, but looks at least a decade younger, not appearing to age since the incident where Hotaru almost died. Whether it's due to Germatoid's possession's effect is unknown.
We aren't privy to her real age, but Athena of Hayate the Combat Butler appears to be the same age as the main character, but the time where she's been staying for the years before her appearance has a different standard of time. When she shows up in the current time, she looks to have aged appropriately since she's been locked out of the castle.
She also acted rather like an adult back when she was supposed to be six.
And her mindset is from even further back. The mindset she instilled in Hayate.
And now she's back at her 6-year old appearance, while even only given the years we've seen she's at least 16.
The Blade Children of Spiral are all the same age, that is, 17... yes, even Rio. She actually uses her youthful, cute appearance to make unwitting enemies underestimate her. (And by the way, although he looks more his age, Eyes is the youngest of them all, despite being the second tallest of the main five and possibly the most intimidating.)
Katsuo of Yakitate!! Japan. When he first appears in the Newcomer Exam, everyone assumes he's a child because of his small stature and boyish appearance. When he makes it to the semifinals, his wife appears to cheer him on, and he reveals that he's actually 31.
Hope Stelar, Geo's mother, in Mega Man Star Force looks more like an older sister. Then again, Geo's only ten or eleven, so she can't be too old. She looks older in the game.
Mina Tepes from Dance in the Vampire Bund is, like most vampires, a definite example. The only question among fandom is how much older she is than the tween she appears to be (lowball estimates place her at her early to mid twenties, while other hints indicate she is at least on the far side of ninety).
Meiko Rokudou from Ghost Sweeper Mikami comes to mind. For most of the manga's run, her insecurity, cutesy look, and the nature of her crush on Mikami could easily make a reader think that she's anywhere from 17-19 years old (Mikami's 20-21). Then, in one of the last story arcs, we are shown Meiko's mother while she's pregnant with her. The thing is that this is the beginning of the story arc describing how Mikami's parents met. So Meiko's probably 22-24...
V.V. from Code Geass looks like a child, due to immortality, but is actually in his sixties.
Also, the twin mechanics Haruko and Ranko◊ Mikagami are supposed to be older than Ryohei◊.
Luffy from One Piece, the 17-year old hero. He looks older when he is serious (and in some of the earlier arcs he was drawn with a mature look) but with his short stature, big round head and eyes, big mouth and small nose it's hard to believe he is much older than 10 years unless you know better. Doesn't really help on the age estimation that he is also a Man Child. After the Time Skip he is now 19, but looks like a 10-year old as much as ever.
Chopper looks like a baby reindeer, while he is in fact 15 (17 post Time Skip). In his semi-human form, he looks closer to his age, but no matter what form he takes, he keeps his child voice in the anime.
In SBS questions, a fan did some maths, and was amazed to discover Franky was 34.
Aokiji may look like he's in his mid-to-late twenties or early thirties, but he's actually 47/49.
Shakuyaku looks like a rather young woman, but she's actually a Retired Badass who quit piracy forty years prior to the start of the story.
Kureha looks to be in her sixties, but she's actually 139. Due to her body looking far more youthful than her Butter Face, a Running Gag with her involves people assuming her to be a young woman until they notice said Butter Face.
Al is one year younger than his brother, but during The Movie he looks thirteen while his brother is an adult. Justified by the fact that when he got his body back he came back as the same age he was when he tried to revive his mother
The Affably Evil priest Rezo from Slayers is the century-old great-grandfather of one of the protagonists, Zelgadis; aside from the two barely-noticable boney lines under his eyes, he looks to be more in his late forties or early fifties. Lina lampshades this when he appears in the first Light Novel, describing him as looking "both young and old at the same time."
A non-human example would be Hellmaster Fibrizo, who is both the oldest and strongest of the world's five Demonic Lords. He disguises himself in the form of an androgynous young boy in order to decieve people.
And from the fourth and fifth seasons of the anime, Pokota the prince has the voice and the demeanor of a 10-year old. In reality, when his kingdom was struck by a plague about a decade before the series proper, his then 10-year old body was sealed away (along with the rest of the country's citizens), and his soul was placed in a stuffed animal. Realistically, he should be a bit older than Lina.
In Bakuman。, Natsumi Kato looks like a high school student or young college student, but she's actually around 30.
Then there's Viral who will become this because of his immortality.
Ryouhei Sumi from Future GPX Cyber Formula looked like he's a little kid, but he is in fact 15 (at the beginning of the series) making him a year older than Hayato, the main character.
White from Tekkon Kinkreet; by the way he looks and acts you'd think he was about 5 years old, but he's 11.
Nene from Bubblegum Crisis Tokyo 2040 is rather short and undeveloped, and tends to act like a young teenager rather than the 20-year old woman she is. It seems to be her Berserk Button, if her reaction when she flirts with her boss (His reply? “I don’t like little kids”) or when 15-year old Makkie comes onto her is any indication.
Reiji Miyabi (aka Head) from Star Driver appears to be about 15 to 17 years old. Flashbacks to the time when he fathered his now 15-year old son, Takuto Tsunashi, suggest he's at least twice that age, if not much older.
Yuka in Kemonozume is about 30, but looks like she's in her early-to-mid twenties. She seems pleased when someone correctly guesses her age.
In the original Cutey Honey, the shape-shifting android Honey was Younger Than She Looked (supposedly 16 but was probably built more recently than that). By the time New Cutey Honey came around, she looked a little older (early- to mid-twenties, probably voluntary aging from her powers), but being over a hundred years old, she had moved to the opposite trope.
Natsu from Fairy Tail is hinted to be this, although nothing's been confirmed yet. During the Fighting Festival Arc, he gets trapped with Master Makarov by a spell that only affects people over the age of 80... but the confusing part is that he's shown to have grown up normally in the past few years.
Yuka of Blood-C. She's apparently old enough to be a politician (which would put her somewhere in early thirties at least) but can pass as a high school student.
The title character of Acony has the body of a twelve or thirteen year old girl, but claims to be 23. Her high school aged neighbor laughs at this, saying that if she's going to lie she should go all out and say she's Really 700 Years Old, but it's true; she was involved in a superhero origin-esque botched scientific experiment that slowed her aging to a crawl. She'll look 23 by the time she's 80, but she'll die around then because her lifespan is still that of a normal human.
Even if almost all of them have a case of Really 700 Years Old, the anthropomorphic countries in Axis Powers Hetalia rarely even look their "human age". England is supposed to be physically 23, but is often drawn not looking any older than 15. In-universe, this is the case for Japan; Italy thinks Japan is too young to drink, when he's actually way older than Italy.
In Arata Kangatari, Princess Kikuri looks surprisingly youthful for a 60+ year-old woman. Justified, as her powers suppress the form of her true age.
All 12 of Abe no Seimei's Shikigami in Shonen Onmyouji are very easily hundreds, maybe even thousands of years old, but most of them appear to be in their mid-twenties or early thirties. The exceptions being Taiien and Genbu, who both look like children.
Daichi is excessively short; when Haruka first met him he was mistaken to be an elementary schooler.
Haruka herself is short among the girls, and her mother often teases her for looking child-like.
Saijou no Meii: Saijou should be in his 20's but he looks about 15 and acts even less than that. Probably to make it easier for the readers to identify with, as the author's stated goal in writing the manga was to inspire young people to study medicine.
Princess Princess: When two of the "Princesses" first met Sakamoto Akira's mother, they thought she was his sister and couldn't even figure out if she was older or younger than him. When he told them she's his mother, he even had to clarify she's not a stepmother.
Waratte! Sotomura-san: Sotomura's mother looks so young people at first think she's Sotomura's elder sister.
Medaka Box: Zenkichi's mother looks like a twelve-year-old girl but she's actually 42.
Futari Ecchi: Shoko Shiina is 24, despite looking like a little girl.
In The Face Burglar by Junji Ito, Kamei is a shapeshifting schoolgirl who involuntarily takes the appearance of anyone she spends time around. It is stated at the end of the story that she is not really a student and has been attending the school without permission, but no one knows how to get rid of her. They believe she is far older than she really appears.
Cassian from Count Cain's growth was stunted such that he looks twelve or so but is an adult. This being a vaguely-Victorian world, he wound up working in the circus for a while.
Kurapika from Hunter × Hunter is seventeen at the start but doesn't look much older than the twelve year olds Gon and Killua.
Biscuit appears to be a 12 year old girl but is later revealed to be a very masculine 57 year old, who uses her Nen ability to stay looking young.
Nanoka in Koi Kaze is fifteen at the start of the manga, turns sixteen a few chapters in, and is eighteen by the end. She can pass for a twelve year old which makes her relationship with someone nearly thirty ever the more squicky.
Being a time traveler stuck in a "Groundhog Day" Loop, Homura of Puella Magi Madoka Magica has an uncertain age. Most fan estimates, based on Word of God (around one hundred loops of forty-five days) suggest her to be around twenty-six years old, next to her middle-school peers. However, she looks the same age as the rest of the cast - in fact, she's actually a Pettanko and the second shortest girl. Explanations, from side-effects of her powers to actual immortality, abound in the fanbase.
AKIRA: Kyoko, Takashi and Masaru were often mistaken for children; even a police officer does this when he saw Takashi. However, the trio is actually in their late 30s, with Kyoko being oldest in her early 40s like The Colonel. This is due in part of taking medicine to keep their powers in check.
Aria from Rising X Rydeen looks like she's in her mid-twenties and compared to the rest of the mostly teenage cast she's significantly taller, bustier and more composed despite being eighteen, only three to four years older than most of them. Takara is shocked when she reveals her true age.
Yukiya from Okane Ga Nai is hit seriously with uke stereotypes. He's an eighteen year old college student but looks more like a twelve year old boy, or a eighteen year old woman.
The Demons in Kyo Kara Maoh! age at a slower rate than humans, and live longer as well making them this. A good example is the main hero's accidental fiance Wolfrem, who is physically a 16 year old, but is chronologically 82.
Toriko was surprised to find out when they were at an island known for its alcohol that his partner Komatsu (who looks like a preteen) is the same age he is — 25.
Hinata Hakamada from Ro-Kyu-Bu! is a sixth grader but looks and acts like she's around seven. Subverted as she does have noticeable breasts.
InuYasha certainly qualifies given that he should be around the age of 200, despite appearing to be around the same age as Kagome. This also applies to demons, in general.
Soul Reapers have vastly expanded lifespans and therefore their chronological ages do not match their biological ages. For example, Yamamoto looks like an elderly grandfather but has been around for over 2,000 years whereas Hitsugaya looks like he's around 13 years old but has been around for at least 40 years. While Rukia looks like she's in the same age-group as Ichigo, she once told his fifteen-year old self that she had lived ten times his lifespan.
Even on the Soul Reapers' Really 700 Years Old scale, there are inconsistencies. During a flashback taking place 100 years ago, Gin Ichimaru and Nanao Ise are portrayed as children, the former looking between 10 and 13, the latter around 5 to 8. Hiyori looks to be about 12-15 in the same flashback, but looks almost exactly the same in the present day. This counts for Mashiro, too.
Hollows don't age at all. As a result, there is no way to guess how old they might be. Lilinette lampshades this when Ukitake refuses to fight her on the grounds that he cannot - will not - fight children. He knows her chronological age has nothing to do with her biological appearance, but he will not change his stance.
In filler, there's Ran'Tao from the Bount arc, who looks to be the Soul Reaper equivalent of a 30-year-old. In fact, she's quite old even by Soul Reaper standards, but through self-experimentation stopped (or at least greatly slowed) her aging at the price of greatly reduced stamina and a need to sleep roughly 2/3 of each day.
Suzu from Seitokai Yakuindomo looks like an elementary schooler, but is actually in high school. She's a little touchy about the subject.
Nanami in Yandere Kanojo is another high schooler who looks like she's still in elementary. This causes problems when she falls for main character Manabu, who thinks she is the age she looks, and treats her as having a Precocious Crush on him.
Also of note is the Principal's wife, who looks as if she's still at school, but was actually classmates with her husband. The other characters even lampshade just how weird it is.
Kanojo ga Flag o Oraretara: School elder Tsumugi Ryuukishibara looks like a young child, complete with bonnet; in truth, she was once a fully-grown woman, but shrank to her current height as she got older. No-one knows how, and Tsumugi herself seems to think it's perfectly natural. Rumor has it she's been around since the school's founding.