Akira is the kind of guy who gets intertwined with shitty guys and needs to break out to make a better life for himself by The Pression. From where I've read up to, him being non-binary hasn't really been mentioned, but it's been confirmed through the character art.
Charlotte
from Air Gear
Trans Woman · she/her
Listen, Air Gear doesn't handle anything the best. It is a very cis hetero male manga with a strangely large amount of queer characters. That said, I really liked Charlotte. There's cheap shots about hitting her in the balls (a move she is impervious to) but ultimately she's a young woman that has been through a lot and committed to being herself through it all. She has a boyfriend that loves her and supports her. For some reason the Air Gear wiki calls her a guy even though it's clearly stated she's not.
Cow
from Cow Life Sim RPG
Trans · Cow
Everyone in Cow Life Sim RPG is trans, so Cow is here just to cover the entire game. Cow Life Sim RPG is an extremely trans welcoming space where it's not about being trans, but everyone is and it's not a big deal. I've never seen any pronoun use for Cow, nor anything clarifying beyond trans, so Cow is just Cow with the knowledge that Cow is trans.
Dashiell De Rue
from Parfum Nostalgique
Non-Binary · he/her
I'm legally obligated to inform you I got a review copy of this game so I guess any time I talk about it it's an ad. I've only played a bit of Parfum Nostalgique, but Dash truly is the scene stealer. He's beautiful, the moment she's on screen it's about her. I love him. The other characters are supportive, though there's some tensions in his life.
End
from Beyond the End
Trans Masc Non-Binary · he/him
I love End - he's just a sweet little sheltered kid having to finally come out and meet the world. BtE doesn't really mention that he's trans, but there's still a lot of theming based around changing names and parts of your identity as you grow into yourself. He is confirmed as non-binary in character profiles, and wears a binder though.
Es
from MIGLRAM
Non-Binary · they/them
Actor's Gender: Cis Female
It's a bit weird to include Es as they are non-binary but they're also possessed by twitter comments so sometimes "they" is "everyone on twitter". The idea of them being non-binary doesn't come up in the narrative so much as a sort of plurality feel from having to hold so many differing and complex feelings. There's a level to their adrogyny that feels like it was meant to bait the listener into treating them like a self-insert, but in the end, non-binary is non-binary.
Jamie
from Harvest Moon Magical Melody
Genderfluid · Whatever Yours Aren't
Quite frankly the funniest one to include. Jamie's gender is set to whatever yours isn't when you start the game, but they're still the exact same character regardless of which you pick, so they are essentially genderfluid and they just really hate you. It never comes up in game, but they may as well count for first non-binary romance option in a Harvest Moon/Story of Seasons game.
Kakei
from Wish, Legal Drug, Drug and Drop
Trans Man · he/him
Kakei first appears in Wish - though I believe some translations use she/her for him. It seems that by Legal Drug, they'd ironed out to having to use he/him and accept him as a guy. One of the weird instances of the translation being a major issue to your trans character. Of course, Kakei has a loving husband, a wonderful son, and also Kazahaya. Not a lot of focus is put on Kakei slotting into a binary gender.
Kohaku
from Wish
Angel · ???
Translations are real spotty with Kohaku's gender. They're also a case where they don't have an assigned gender at birth so not technically trans, but I'm including them for the people who want non-binary characters. A lot of people are confused by Kohaku's gender, and when asked they just say they're an angel. Most the major cast are understanding (or angels/demons themselves), but it comes up sometimes.
Kizzy
from HiGH&LOW
Trans Woman · she/her
Actor's Gender: Cis Male
HiGH&LOW isn't like. Good. and Kizzy isn't in a lot of it. But she is supported by everyone in the show and has a boyfriend that loves her very much. Kizzy helps rescue people from human trafficking.
Gin Noto
from The Caligula Effect 2
Trans Masc Non-Binary · he/him
Actor's Gender: Cis Male
Everyone I know is in love with him. Lot of people really happy with the game's presentation of a non-binary character - tackling his dysphoria when being read as a man or a woman. Game also showcases a lot of struggling to adapt around toxic masculinity, though Gin can be a bit lax with some of his male friends.
Meiko
from Hashihime of the Old Book Town
Trans Woman · she/her
Actor's Gender: Cis Female
Handling of Meiko (of the Meiji period) is a little interesting in introduction? Protagonist is kinda shitty but he's also a shitty person in general but he comes round and does a bit of the misguided cis stumbling and tries to get her some gender surgery for free without asking. Her taste in men is awful, but she's so fun and smart I love her.
Nagi
from Raise de wa Chanto Shimasu
Trans Woman · she/her
Actor's Gender: Cis Male
Raisechan isn't good for trans rep - lot of the characters are really shitty towards Nagi... but I can't help but love her lmao she may have a shitty sorta boyfriend and she has to train him but she's just so charming in her own right.
Oshima
from Kafka on the Shore
Trans Man · he/him
You probably shouldn't read Kafka on the Shore, but Oshima getting in a fight with TERFs because they came into his work is certainly a scene that happens. It's not well wrote and when I read it it felt like a strawman of feminism but... over time I've seen TERFs making these as real arguments so thank you Oshima for kicking TERFs out your work. Guy who outs himself just to win an argument. The narrative is pretty confident treating him as a guy as well, but there's much more questionable stuff to worry about in this. Oshima who is trying to be open-minded about love vs this kid who has some sort of incest fixation.
Someone
from Our Dreams at Dusk: Shimanami Tasogare
None · Any
I think there's something fascinating about the depiction of Someone. There's a dissociation even in themself, where they're both treated as ephemeral and act as though they are, but in the end, they're just another person. Their sense of self is only fully realised by being as labelless as they can be, to the point that it can feel wrong to try to categorise them. Everyone loves Someone, but Someone keeps their distance because that's what they want to be. Everyone uses she/her for them (at least in the English translation), so for much of the series it gives the impression they treat her more as a woman, but it doesn't seem malicious.
Saiga
from Wish, Legal Drug, Drug and Drop
Trans Man · he/him
Saiga first appeared alongside Kakei in Wish, though there was never any issue with translators misgendering him. Saiga is another one that technically didn't have a gender at birth, but decided he was a guy after coming to Earth and living as a human.
Sapphire Sasaki
from Uuultra C
Trans Man · he/him
Actor's Gender: Undisclosed
Everyone except his mother is very supportive of him; she introduces him as her daughter, though calls him Sapphire and does clearly care a lot about him. She gives a bit of a "doing her best but not quite getting it" feel. When he reintroduces himself as a boy, everyone accepts it without question (to the point I just accepted his mum had lied for some reason) and the people around him aren't pushy about gender conformity; encouraging him to have fun expressing himself in whatever way he enjoys, letting him wear make-up without treating it as a strike against his identity.
Sonoshi
from Avataro Sentai Donbrothers
Non-Binary · ???
Actor's Gender: Cis Male
We guess Sonoshi is non-binary; it never came up in the show and everyone hates their ass for being annoying.
Suguru
from Digimon Story Cyber Sleuth
Genderfluid · he/she/they
No, Suguru isn't a character that even gets a unique model, and they exclusively appear in a random optional side quest - but they are non-binary! They started hacking because Eden didn't allow them to switch their avatar's gender whenever they wanted and didn't allow multiple accounts, so it was the only way they could switch their avatar as needed. They did get into date scamming though. They come out to their brothers who end up accepting them!
Stephanie
from Sorcerous Stabber Orphen
Trans Woman · she/her
Actor's Gender: Cis Woman
Stephanie is honestly the best character in Orphen. Even though she's lost her magic, she competent, smart, and they'd be lost without her. Unfortunately, the cast can be transphobic behind her back, but they're at least respectful most of the time. Note : Stephanie was wrote out of the more recent anime and I haven't got to her in the light novels to know how she's handled there.
Suzu Isshiki
from Uuultra C
Non-Binary · he/him
Actor's Gender: Cis Male
Hottest girl in the world holy fuck. His husband is a transphobic piece of shit but quite frankly every trans person in the area is coming over to kick his ass (and he'll fight anyone who calls his wife a slur; only he gets to do that). Suzu has the dysphoria of being raised as a girl for a bit and having a lot of positive connections with how he was treated and still clinging to that, but growing up and puberty and not disliking being a guy and feelings just getting so mixed up in dysphoria. Another one I've found my non-binary friends like.
Sweet-P
from The Caligula Effect
Trans Woman · she/her
Actor's Gender: Cis Woman
Sweet-P's depiction is rough. She's in an extremely unsupportive environment with people who misgender her regularly. But, I actually really love how her story ends up going. There's a focus on the idea of transition goals and the fact that even though Sweet-P wants to be a petite girl, she doesn't enjoy the process of dieting, etc. She has to re-evaluate her goals and get that kinda idea a lot of people talk about of "you gotta accept you'll probably look like someone's mum." It's not an easy story to go through, but I think there's a heart in it that makes me really fond of her story.
Uran Miyamoto
from Uuultra C
Intersex Trans Woman · she/her
Actor's Gender: Cis Female
I know this one's kinda controversial to say but. Uran would of been amab, even though she's intersex but she's made it clear she's a woman so I think that counts. Everyone is supportive around her even if Shirou is shocked. While the word choice for an intersex character isn't perfect, body descriptions don't feel completely inaccurate from actual intersex bodies.
Utsumi Natsuyoshi
from Our Dreams at Dusk: Shimanami Tasogare
Trans Man · he/him
Honestly, Our Dreams at Dusk is just so good. Utsumi has a supportive found family that he can rely on and that desperately want to step in when he runs into old friends who misgender him or treat him like some medal of their own open-mindedness. He's kind and supportive, but even he can be pushed to snap when he's not being treated like a person. I truly love him so much.
Zoe
from Monster Prom
Trans Woman · she/her
Actor's Gender: Non-binary
It's been a long time since I played Zoe's story, but absolutely here for agender-to-female and that kind of idea of gender still being something people want to opt-in to. Finding something that resonates with your identity in that sorta way.
Yoite
from Nabari No Ou
Intersex Trans Man · he/him
Actor's Gender: Cis Female (Japanese), Cis Male (English)
It's been so long since I read Nabari No Ou so I can't comment with complete confidence, but I remember really liking Yoite and an intersex character that is also trans.
The characters listed here are purely characters Marine has a familiarity with enough to speak on. There are plenty of other places you can find more trans characters! If, however, he’s forgot a trans character that you know for a fact he knows, please prompt him to add them.
Where can I find more trans characters/commentary on trans characters?