Everyone in Asura's Wrath. The story takes place over the course of 12,500 years. None of the characters seem to age a day during that time frame. Justified, as nearly every named character is a god.
The character named "Jr." in the Xenosaga series appears to be twelve or thirteen years old, but is actually twenty-eight. His genetically engineered powers caused him to be physically stuck with a kid's body due to a major trauma when he was actually that age. He has a clone twin brother, (well, two, actually, but let's not get into that) who is younger by a small margin but has aged normally, and at one time chides him, "You're older than I am. Try to act like it sometimes".
If you choose to date her during the summer festival, 15-year old Ayane Matsunaga from Persona 4 is mistaken for an elementary, then middle school student by one of the vendors. To add insult to injury, when she wins a book in a festival raffle, the host politely warns that it may be too difficult for her to read. She doesn't take it very well.
According to Grienko's notes in Second Sight, the psychic Zener Children are afflicted with a developmental disorder that has stopped them from aging past puberty. Since Project Zener has been active (if not funded) for several decades, this would place most of them in their forties or fifties.
Resident Evil 4 has a rare case where both this trope and its opposite are valid with Ramon Salazar. While most players assumed he was a child no older than 11 playing dress up, Leon looks at his wrinkled skin and gray hair and thinks he's a withered old man. Both are wrong — Salazar claims to be 20 years old.
Resident Evil 6 has a straight example in Sherry Birkin. She's 26 years old, but looks, sounds and frequently acts slightly younger than her escortee Jake Muller, who's 21. Justified in that it's an effect of the G-virus she has in her adapting to her body and increasing regeneration to Healing Factor levels.
Presea Combatir had her biological and mental growth stunted by a magical implant for 16 years, leaving her a 28-year old with the body and (heavily traumatized) mind of a 12-year old. Due to her circumstances, she is treated much like a Human Popsicle by the rest of the cast.
Tales of Symphonia: Dawn of the New World has Alice. In one of the skits Marta (who is 16) explains that Alice, who looks younger than her, is actually older by two years. Alice flaunts her cuteness constantly, much to Marta's annoyance and Decus' delight.
Pascal from Tales of Graces is supposed to be 22 years old. Considering how she looks and acts, this is pretty hard to believe. To say nothing of the 40-year old Malik.
Tales of Destiny 2: Judas looks to be in his late teens/early twenties, and it causes problems when he has firsthand knowledge of places, people, and events he shouldn't have even been born in time to see (he was brought Back from the Dead and displaced in time). Discussed when Loni demands to know how he could possibly know what he does and be in his teens, and he brings up this trope. His actual age is 34.
Path of Radiance and its sequel, Radiant Dawn, has a few characters are described as "Branded", meaning they are a result of a taboo union between the two races in the game: laguz (shape-shifters) and beorc (normal people). While the branded are most like the beorc, they generally age slower like their laguz forefathers. As branded are shun by laguz and beorc alike, they cannot settle down, and need to hide their brand (which can be difficult if it shows up on, say, the face).
Finn from Fire Emblem: Genealogy of the Holy War, is 35 in the second generation and 34 in the related game Thracia 776, but in both he looks like he is only in his early-to-mid twenties. It becomes especially apparent when you compare him to Glade and Oifey, who are in their mid thirties and look their age.
Laurent, in Fire Emblem Awakening: Even though Lucina is the first-born of the second-generation characters, when she and her companions traveled back in time, Laurent wound up being sent three years earlier in time than everyone else. Hence, as a result of this minor time-travelling mishap, he becomes three years older than Lucina by the events of the game.
Krile's battle sprites in Final Fantasy V are the 'child' type used for preteen characters Rydia, the Mysidian twins, and the Onion Knights from the previous two games (which use a three-quarter Aside Glance to make the face look bigger). She's actually fourteen, which is only clear in the Amano art and larger, Amano-based portrait from the mobile port.
Vincent Valentine of Final Fantasy VII appears and is listed in all game materials to be age 27, but that fails to factor in the thirty years he spent sleeping in a coffin. As his age in all future installments has failed to increase like the rest of the cast's, it can be assumed that the bizarre experimentation Hojo subjected him to has sealed his age.
Vincent's love interest Lucretia is just about as old as he is, but thanks to Jenova cells she still looks just as young.
In Dirge of Cerberus, Vincent meets Shelke Rui, a new character (and possibly a new love interest). She's a 19-year old whose body stopped growing at age nine as a result of various experiments she was subjected to by Deepground.
As of Final Fantasy VII: Advent Children, Sephiroth is 32 but stopped physically aging at 25 (that's what you get when you go several years without having a physical body at all).
In Final Fantasy XII, Fran's sister reveals she left the village fifty years ago. This revelation is later played for laughs, with Vaan being utterly (and understandably) confused by this information.
Rydia in Final Fantasy IV: The After Years is probably in her forties or at least her late thirties, since she was an adult at the end of Final Fantasy IV, and TAY takes place seventeen years later. Nonetheless, she retains much of her youthful appearance and mannerisms.
Rekoteh and her brother Rolan from Final Fantasy: The 4 Heroes of Light are Dragoniers, who live much longer than humans. Their exact age is unclear, but Rolan is at least 300 and Rekoteh looks exactly the same in both past and present.
In the original .hack// series, Mistral appears in The World as a young, perky Wavemaster. In the real world, she is a twenty-something housewife who's pregnant with her first daughter.
Mortal Kombat X; after a 25-year Time Skip, Sonya Blade still looks rather young and attractive, despite being in her forties and having a grown daughter. (She has, however, lost the Stripperific costumes.
In The Legend of Zelda: Majora's Mask, Kafei is a grown male that is about to be married to his fiancé. He comes across Skull Kid, when Kafei doesn't play with him Skull Kid transforms him into a child, he spends the game in hiding or covering his face with a mask.
Fiona of Arcana Heart, who stopped aging after she was pulled into the Elemental World, so while she's approximately as old as Saki, she still looks like a little girl.
In Secret of Evermore this trope extends to all four of the human characters who have been trapped for thirty years in the virtual world of Evermore, since nobody physically ages there, but it particularly comes into play with Elizabeth, who was 10 years old at the time of the experiment. When the present-day hero's accidentally transported into Evermore and meets her, she's become the ruler and protector of a prehistoric village, and has a mature, mentor personality that's completely at odds with her appearance.
Lymle from Star Ocean: The Last Hope looks and acts around six years old, but really is around 15 due to both the size of her people in general and from an accident with symbology that caused her to fall into a demon portal and suffer so much hate and miserly she cut off all of her emotions. (This is only revealed in the in-game encyclopedia.)
Shadow the Hedgehog is 50, but that's just the time he's accumulated being preserved in a machine on Prison Island. Apparently, he shouldn't even be two. Funny, considering that he curses up a storm in his game...
The Deadly Six from Sonic Lost World look fairly young for aliens (except Master Zik). You'd think they'd be in their teens or early 20's, right? Well, Zazz alone has been stated as being over 127 years!
In Super Smash Bros. Brawl, the Mother/EarthBound series characters Ness and Lucas are depicted as looking very young, when they are actually supposed to be teenagers. It's justifiable in that their original in-game sprites and character models look like children, but it's still pretty funny when you see just how short they are. It's especially evident in the Subspace Emissary scenes where Lucas and the Pokémon Trainer are traveling together. According to the Pokémon series canon, Red is eleven years old when he starts his journey and yet Lucas, who could be at least 2 years older than the Pokémon Trainer, is half his height.
To an extent, some of the protagonists. In canon, most of them are around eleven years old from the looks of it but several look a bit younger.
Emma from Pokémon X and Y is probably a better example. She's made to seem far younger than the roughly fifteen to eighteen year old protagonist, appears shorter than you, and is the leader of a group of kids who dislike the protagonist for being "too grown-up"... But she's explicitly sixteen years old. Most fans thought she was Shauna's age or younger.
Marshall Law in Tekken 6 looks younger than 49, and even fans speculated that could be his son Forest in disguise.
Lee Chaolan looks like he's in his late twenties to early thirties. He's actually 49, but it isn't really surprising to fans, since he was in the first two Tekken, and the newer games take place 20 years after Tekken 2. But for people new to the games, it's a bit surprising.
The queens of this trope for this particular series have to be Nina Williams and her sister Anna. Both are 42 years old biologically, but spent the 19 years between 2 and 3 in cryogenic slumber, which explains their early 20's-ish appearance.
Jun Kazama, especially in Tekken Tag Tournament 2, which came out over a full decade after the first Tag which subsequently was her last appearance. Seriously, for someone who's lived for almost 40 years now, she is glowing. And that's without cryogenic sleep.
Even more jarring, she's Jin's mother. She looks like she could pass off as his sister!
Most of the human race is this in Mass Effect, due to vastly improved medical technology and genetic engineering. Miranda is highly generically engineered and looks easily in her 30s while actually being almost 40. Kahlee Sanders is in her early forties, but appears to be in her early thirties. The Illusive Man looks fairly young but is implied to be much older.
Serval of Mortal Kombat's characters reach the ages of 10000 and higher via Kitana and Sindel, but you wouldn't know this by looking (Kitana looks to be in her early 20s while Sindel is at her late 40s). As of Mortal Kombat X, a Earthrealmer - Erron Black fits this trope, due to a process of gaining the Edenians' long lifespans thanks to Shang Tsung. And if his ending is true, Johnny Cage is about to pull off this trope as well.
The Jedi Exile from Knights of the Old Republic 2; according to Mira, the Exile's appearance hasn't changed since the Mandalorian Wars, ten years prior to the game. This would put the Jedi Exile in her thirties at least.
Tonnio and Liina in Phantasy Star Universe both look like 12-year old kids but are actually on their late twenties, which came as a surprise in Portable 2 when they are a married couple.
Pretty much everyone in Mr. Driller looks older than they look, mostly the teenagers, all of them look like they're 11 years old or so, most of them are already 14 or even 17.
Isaac and Garet look about ten in the prologue, despite being supposedly around fourteen. They still look fairly young three years later, and join forces with Ivan, who is fifteen but looks around ten. Felix on the other hand looks much older, but is stated to be 18 (post-timeskip) in the manual.
It's a plot point for Piers, who comes from a nation which has the secret of prolonged youth, and makes a point of refusing to tell anyone how old he is for fear that it will change how his friends treat him, implying that he's a lot older than the young adult he appears to be.
Becomes a plot point for everyone else in Dark Dawn, as Alchemy exposure has caused the major characters of the first two games to age much more slowly. As a result, Isaac and Garet are now in their late forties and look to be in their mid-twenties, and Kraden, while seventy to begin with, still looks exactly that, despite being over a century old. And of course, Alex still looks around twenty, despite being in his mid fifties...
Dark Dawn still has some straight examples though: Rief looks like a small child but is probably in his mid-teens, Amiti looks closer to fourteen than nineteen-ish, and Eoleo is supposed to be over thirty, but looks closer to his mid-twenties (and again, an inversion shows up— Briggs has gone from his mid twenties in The Lost Age to looking about Kraden's age in Dark Dawn).
While Touhou mostly goes with Really 700 Years Old characters, there are still some that fit this trope. Patchouli, for example, is "only" about a hundred (or has been living with Remilia for about a hundred years; it isn't definite), Rinnosuke merely ages slowly instead of stopping aging all together, appearing identical when Marisa was a child but being laughably young by Gensoukyou standards, and Sakuya appears to be somewhere in her twenties but is noted as being far too mature and worldy to be so young.
The Kingdom Hearts trio in their first game, and subsequent gang appearances featuring said designs. Sora and Kairi especially, who are fourteen but could pass for eleven or twelve-year olds; it's probably Artistic Age and symbolism. Riku less so, since he's muscular and Bishōnen. The biggest contenders for this, however, were Tidus and Selphie. They're the same as as the trio, but look and act years younger; like seven to nine years old, though Tidus does have some muscle on him.
Tira was 17 during the events of Soulcalibur III and IV. Seventeen years later in V, she looks like she hasn't aged a day, thanks to malfestation halting the aging process of her body.
The Kongou-class sisters in Kantai Collection - Kongou, Hiei, Haruan, and Kirishima - are a bunch of quirkyfast and hard hitters. They are also THE OLDEST ships in the entire IJN fleet. Historic note Bar one ship, Asahi, who was built in 1898 and launched in 1900, but she's a converted repair ship by the time WWII rolled in.
Pretty much all of the shipgirl in the game are Older Than They Look anyway. Especially the destroyer and submarine, who's look like grade-schooler or middle schooler.
The Witcher: In a World where there are a ton of long-lived races (elves, for example, naturally live for thousands of years) and magic, it's only naturally that even humans often get unusually long-lived and/or young-looking for their age.
All witchers age slowly due to the mutations that make them witchers.
Geralt looks like a fit man in his late twenties, though by the third game the Art Shift makes him to look about forty-plus. By putting pieces of Back Story together, you can place his age at 80 at the youngest. And if the Witcher in the Distant Finale of Season of Storms is indeed Geralt,note The man could also be Vesemir, but Vesemir dies in the third game. Of course, the books and the games are technically separate continuities, but still… that would make him 200+.
Vesemir, the Old Master of the witchers, looks like about sixty, but has a physique that makes 30-year olds green with envy. Vesemir's age is unknown, but is implied to be pushing eighthundred!
Dandelion the Bard. As Triss so eloquently puts it: "You are 40,note In fact, by the third game Dandelion is pushing fifty. sound like you're 30, look like you're 20, and act like you're 10!" And she's actually quoting Dijkstra, the Dandelion's one-time Spy Master boss, from a somewhat earlier time:
You are almost forty, look like almost thirty, think you're twenty, and behave like you're not even ten.
Emhyr, if we add all the clues from the books, should be somewhere in his sixties, but is depicted as a forty-something man in the third game.
Human wizards routinely extend their lifespan through magic, and given that most advanced medicine in their world is their province, they also have much better health than the general population. Yennefer, for example, Is said to be 92 at the start of a saga,note Though being an elf quadroon, she'd probably have a longer than normal lifespan anyway and the oldest living human sorcerer (at about 1000) got a short "screentime" during the Thanedd coup, though he was already an extremely old man who was described as ready to keel over at the slightest provocation, and, naturally, didn't survive the event.
Radio advertisements in Grand Theft Auto: Vice City mentions a show called Just the Five of Us, featuring a character called Jimmy who looks 12 but claims to be a 42-year old investement banker. This turns out to be real, in show and out in San Andreas, about 9 years later when we hear the actor who played Jimmy again, still looking and sounding like a kid, even though he's in his fifties.
As for Scout, you'd think that he is 17-19 years old, but the description for the Track Terrorizer outfit confirms that he's 23.
Xenoblade has the Nopon; with their Ridiculously Cute Critter looks, Cheerful Child attitude, and You No Take Candle speech pattern, they make incredibly hard to guess their age. Case and point: Riki, the Nopon party member, leaves a dumbfounded look on the rest of the team when they discover he's 40 years old, married, and has several children under his care.
In FEAR Alma looks like a young girl in her pre-teens. At least, until she escapes the Vault; then she looks like a young woman in her late teens. Technically, she was in her mid-twenties when she was killed, but her mind was powerful enough to remain intact, and as of the timeframe of the games she is roughly in her late forties.
The goddesses in the Neptunia series look like teens and preteens (even children for the youngest ones) and even act the part, but they are actually hundreds of years old. Even by their standards, though, Nepgear doesn't look that much younger than her older sister Neptune (She arguably looks older, even).
This gets a Lampshade Hanging in Victory where the alternate dimension's goddesses are made, not born. Neptune wonders where this timeline's version of herself is, only to be reminded that without immortality as a safety net, her laziness and self-negligence probably resulted in her starving to death in the streets. Her reaction to this is priceless.
With few exceptions, the characters in Eternal Sonata are noted for being either this or younger than they look, due to the game's graphical style.
Elliot and Claris from Ni GHTS Into Dreams are actually supposed to be 14-15 years old (15 in Japan, 14 in America and Europe), but yet they look more like 11-year-olds.
Leanne from Resonance of Fate looks about 16 at the oldest, but is actually 21. There's nothing supernatural at work in this case, just puberty having been extraordinarily unkind to her (something she's touchy about).
Its revealed that Meu's appearance in Cross Edge is her younger self 20 years ago, since everyone in the story is in soul form, not actual physical bodies.
An important plot twist in Betrayal at Krondor. An NPC you keep running into all over the map — Squire Philip — looks no older than 20, while he really is close to 40. Prince Arutha appointed him a head of a secret force guarding the kingdom's most dangerous secret. Even Arutha's most trusted officers are surprised when they learn that.
Even ignoring the Artistic Age that plagues the series, Harvest Moon has always had young looking bachelors and bachelorettes:
Subverted with Lumina from Harvest Moon: A Wonderful Life. She is as young as she looks, only being fourteen in the original game. She was Age Lifted to sixteen (eighteen internationally) in Another Wonderful Life when she became Rock's love interest. Harvest Moon DS ignores the awkwardness and uses her adult design from the start. Played straight with Rock himself, who is in his early twenties but looks and acts like a teenager. In a non-Love Interest character, Hugh is eight but looks six. That is because he was six in Japan but was given an Age Lift internationally due to Values Dissonance concerning how his father trains him at his young age.
Katie from Harvest Moon Save The Homeland is one of the few who is mentioned in-series. Her Berserk Button is being mistaken for a kid. Though, she doesn't look too young. It's likely her lolita fashion way of dressing and height that make her look young.
Rune Factory continues the trend begun by Harvest Moon, with character designs that tend to look young for their supposed age. In Rune Factory 4, for example, Kiel is a marriageable bachelor yet looks only ten or twelve. Amber and Xiao Pai are available bachelorettes, but they also look about ten or twelve.
Speaking of Mario, there's Lemmy Koopa. He looks like a cute little kid but he's actually the 'second oldest.' It really does not help that he is very immature, and Iggy, who originally looked like him but with glasses, but was actually two times younger, became an extremely tall green-turnip-hairedMad Scientist!
The protagonist Fang in Fairy Fencer F does look like he's in his late teens, but according to the artbook, he's actually 20 years old. Compounded by Pipin calling him "seinen" instead of "shounen".
In Front Mission 5, by the time of the final mission, Walter Feng and Lynn Wennwright are both hitting their early fifties, but look like they're still in their twenties.
All the younger party members from the MOTHER series are thirteen-ish. Due in part to the games Peanuts-like art style, they all look no older than eight.
In Robopon, when Rena leaves behind her adoptive parents in the second game, she also leaves behind a sphere that makes them young and healthy again while allowing them to retain their memories. While her father becomes something akin to a cute boy, her mother becomes very, very pretty.
As the image on top shows, Viridi in Kid Icarus: Uprising looks like she's eight years old, but it's actually an immortal goddess. Other characters in the game follow that same logic, including Pit, who is at least older than 25 years but looks (and acts) like a 13 year old boy. note though Palutena implies all the divine beings in the game (Yes including Pit) are Really 700 Years Old.
Star Trek Online: Biographical details given for Commander Tiaru Jarok, captain of the Romulan Republic flagship RRW Lleiset, state that she was an officer in the Romulan navy during the Dominion War, which makes her a minimum of fifty-something in STO's present. She looks to be in her late twenties at most, probably attributable to her being Romulan (a Vulcan subspecies, therefore having roughly twice the lifespan of humans).
In ArnoSurge, Cass looks like a Child, but is actually older than 20. Same goes for Sarly, who looks even younger than Cass, but is actually older than her. It's explained that they stopped aging due to "Artificial Incarnation".
Ashley from WarioWare is a teenager in international localizations but her age is unknown in Japan. She doesn't look anything like a teen. Her stylized art in Game & Wario has her looking more like a teenager but normally she looks 9-Volt's age.
Kane from the Command & Conquer: Tiberian Series hasn't aged a day in the almost 100 years of the expansive conflict between GDI and Nod. He is not exactly human though...
In a more minor example, Loghain can appear in Dragon Age: Inquisition if he survived the events of Dragon Age: Origins. The game is set in 9:42 Dragon, and Loghain was old enough to join the Fereldan Army and become its general before the start of the Dragon Age (42 years earlier). He has to be at least 60, yet he still doesn't have as much as a gray hair, and otherwise looks to be in his late 40s or early 50s.
This seems to have hit most of the returning characters as well, who show little to no obvious signs of aging the decade or more between appearances. Special mention to Cassandra who looks to be somewhere in her 20s, but her real age is somewhere in the realm of late 30s to early 40s. She never mentions a number, but casually admits that she hasn't been a "young" woman for a good while.
Meanwhile, Leliana was born shortly after the Orlesian occupation of Ferelden meaning she is probably in her late 30s as well.
There's also Hawke who doesn't age at all through 7 years of the game! Especially true for their default appearances where they continue to look to be in their early to mid 20s the whole time, it's even carried into Inquisition where they would have been ten years older than when they started the game.
In The Order: 1886, all of the Knights including the protagonist Sir Galahad are far older than they appear thanks to the Blackwater. Rebel Leader Lakshmi is also this, since she has the Blackwater that once belonged to one of the original Knights of the Round Table. She looks about the same age as her subordinate Devi, whom she calls "daughter" at one point.
Elizabeth Greene from [PROTOTYPE] looks like a 20 something woman but, due to her being infected by the Redlight virus, is almost 60 by the end of the game without any significant aging. Her son, also infected by the same virus, looks like a completely normal five-year old kid but is actually 40.
Miss Momoka from Omega Quintet is actually billed as "Eternally Seventeen", and looks the part. In reality, she's... approaching a significant milestone. Asking her about it is a bad idea.It's hinted she's pushing forty - the most likely exact number is 37.
Gyromancer's protagonist, Rivel Arday, looks like a fairly young man, but as The Archmage, he's actually at least a hundred years old. Some people believe he's immortal.
Tia from Potion Maker has pretty adult proportions despite being younger than Pio. Pio notes it as unusual and possibly a result of magical potion.
Due to the setting of Caligula, while all the characters appear to be high school age, quite a few are older. Some of them are more drastic than others; for instance, Mifue is 17 instead of 16, but Shogo and Kotono are adults (30 and 23 years old, respectively), and Kensuke is 19 years old.
In Piratez, Hellerium-depraved Ubers are small and cute, but in fact they are usually older and wiser than your average, big Ubers.