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.
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.
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.
Krile's sprites in Final Fantasy V make her look ten or twelve because she's the resident Badass Adorable. The artwork and the portrait from the iOS port make it more obvious that she's actually fourteen.
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.
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.
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, The Obi-Wan 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.)
Sonic the Hedgehog: 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 Pokémon protagonists. In canon, most of them are around eleven years old from the looks of it, but several look a bit younger. The Black and White protagonists are supposed to be older, though.
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.
Jaguar from Space Channel 5 doesn't look much older than Ulala and Pudding who are respectively 22 and 19, though he's actually 35.
Carlie of Seiken Densetsu 3 looks like a toddler. She's actually 15, because she's a half-elf. The half-beastman Kevin fits too, although not quite to the extent of Carlie.
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.
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, stated to be 18 (post-timeskip) in the manual
Becomes a plot point 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 there's no way Eoleo is over thirty (and again, an inversion shows up— Briggs has gone from his mid twenties to looking about Kraden's age).
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 12-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 - nine years old, though Tidus does have some muscle on him.
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.
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.
Several Harvest Moon characters. Nina from the original game looks and acts more like a ten year old then an adult, Ann from Harvest Moon 64 and its similar titles doesn't seem much older than sixteen, and Pierre from Island of Happiness and Sunshine Islands looks a little kid. Luna in her original Tree of Tranquility is about half as tall as Kevin and has to jump in order to kiss him on their wedding day. She combined with her lolita style of dressing makes her look quite young, twelve or under. In the Alternate Universe that is Animal Parade she's considerably taller though, but still looks somewhat young due to her fashion. Kate suffers from the same thing but she's explicitly referred to as looking younger than she is.
Lumina from Harvest Moon: A Wonderful Life is an unusual case. In the original games she was thirteen years old, and while looking a bit young for her age that's not anything too off. But come the Distaff Counterpart and she's upped to age sixteen in Japan, age eighteen everywhere else, in order to be paired with Rock who is twenty-two. They did however not change her design and all so she still uses the model of her early teens self◊. A Wonderful Life: Special Edition plays this even worse as they play off Lumina's romance as a Precocious Crush for the most part.. Except you can marry her. After you get married it skips to the normal 3 or so years later and Lumina is in her adult design, which she normally shouldn't be in until your child is several years older. DS and Cute don't even use her child design, just using her adult design off the bat.
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.