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  • The protagonist of After School Nightmare is an intersex boy. The first page in the manga has him averting No Periods, Period, much to his discomfort. She later identifies as a female, but then it turns out she was never actually an intersex person at all, but was actually two people. It's complicated.
  • The main character from Ai no Shintairiku, Sara Nikotama, is a trans girl high schooler who falls for a boy at her new school.
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    • Arakune/Arachne, who doesn't have reassignment surgery because it'd mean she would lose some of her strength. Whether Arakune is trans or simply prefers crossdressing is a little bit unclear. Yuki-sensei used some terms early on and then switched to using others later, and with the time period, limited research material available, and the natural evolution of trans language, it's all but impossible to tell now.
    • Sevothtarte/Sevy, previously named Laila is a trans man... sort of. In this character's case, it's as a result of the trauma of being gang-raped, living in denial of her previous existence as Laila, and goes as far as undergoing treatment to inhibit her breasts. She also wears a machine that makes her voice sound 'masculine'. This results in some Unfortunate Implications and wouldn't be a good example, except that Yuki-sensei played with gender and sexuality in several other characters in the same series.
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    • Belial, the Mad Hatter, explicitly identifies as neither male nor female and deliberately resorts to genderfuck clothing and make-up to play on their androgynous appearance. Some scenes shows them as more masculine or feminine than other ones, though; in the presence of Kira or Lucifer, Belial usually looks very much like a wounded Femme Fatale. To make this powerful Trickster character even more complex in terms of gender and sexuality, Kaori Yuki also makes them omnisexual, madly in love with Lucifer, seduces Kurai partly by taking the appearance of one of her male suitors and generally acting like a campy male.
    • Kurai herself has some trouble in identifying as female, although it's probably partly because she starts off as a young teenager. She seems to have less trouble with her gender identity once she 'develops' at an extremely quick rate. However, she explicitly compares herself to Arachne, mentioning that their families had problems with Arachne being what they thought was a 'transvestite' and Kurai being a 'tomboy'.
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    • Alexiel and Rosiel. While she laments to have been "born female", because she had too many feelings to deal with and wished to be reborn as male (which led to her reincarnation as Setsuna), she seems to embrace her true self in the end, she still has gender issues. Meanwhile, her brother wants to be her, he has her beauty/face and even pretends to be female once.
  • Sechs from Battle Angel Alita, who is a transgender robot. Originally a member of the "Tuned" series, mass-produced copies of Alita's cybernetic body with an AI instead of a human brain, Sechs decided at some point to start referring to himself as male because he thought it suited his personality better, gradually upgrades his body with more masculine-looking components and eventually has his Personality Chip transferred into a fully male technorganic body. The odd thing is that none of his "sisters" seem uncomfortable with their assigned gender, though Alita once thinks she'd probably have an easier time concentrating on fighting and not worrying about emotional concerns if she'd been born a man.
  • Black Butler: Grell Sutcliff, who seems to behave like a flamboyant okama, is actually a trans woman. This is made clear when she sympathized with Madame Red due to their similar inability of giving birth. This also makes her the only member of the known Shinigami who identifies herself as female.
  • Black Jack: Kisaragi Kei. He was formerly a woman called Megumi, but after having a cancer that required removing his uterus, he begins to present himself as a man and adopts the masculine identity of "Kei". As seen in this manga page, he tells Black Jack that he is happy he quit being a woman. And although the fandom is heavily debated on this, as he can also be seen as simply a Bifauxnen woman, the manga seems more adamant in portraying him as being trans.
  • While not actually present within Boku Girl, as it features boy who was Gender Bent, characters who are aware Mizuki is physically female but not that he was originally male usually take his declarations that he's a man as falling under being transgender. Another character, his crush Fujiwara, knows for a fact he was male but then has seen him doing things like wearing dresses (to visit a bathhouse away from his all-male dorm) or wearing panties (his roommate hung his regular underwear to dry in the rain) and thus comes to the opposite conclusion that Mizuki is a trans woman.
  • Marika of Bokura no Hentai is a transgender girl. The other two main characters are crossdressers she met on a site for crossdressers. Not soon after her voice starts cracking she comes out to her mom who starts visiting a hospital with her. After seeing a therapist she begins living as a girl.
  • Jun's mother in Boku to Boku is a trans woman. Jun became a Wholesome Crossdresser because his Fashion Designer mom would try out clothes on him. He originally hated it but eventually gained a taste for feminine attire.
  • Alice Arisuin from Chivalry of a Failed Knight is a non-operative trans woman. Her fellow mains quickly just accept that that's part of who she is.
  • The protagonist of Riyoko Ikeda's Claudine...!, Claudine de Montesse. He's a very woobie-like trans man with a sensitive heart and horrible luck, who ever since he was a child was sure that he was a male, and in the end commits suicide after his lover Sirene gets engaged to his eldest brother Andre. His doctor (who doubles as Narrator All Along) reminiscences about Claudine's case, and concludes that he was right into identifying as a male.
  • The one-shot Cotton Candy Love is a Yuri Genre manga with the most major character being an elementary school aged trans girl, who gets bullied by classmates.
  • The Day of Revolution is a two volume manga series about an intersex but genetically female high school boy who elects (under pressure from his family) to become a girl because he sees it as a choice between being an 'incomplete man' or a 'complete woman'. He quickly finds that letting go of his old male identity isn't going to be easy or simple.
  • Chaplin from the Deadman Wonderland manga is transgender. The first time she used her Branch Of Sin was when she was living as a male. Her lover was using her as a source of money and she got mad at the woman he was sleeping with. She accidentally stabbed her, which is why she's in jail. Chaplin was Adapted Out of the anime.
  • One episode of Dirty Pair featured a wealthy business owner framing his son's fiance for kidnapping when really they were trying to elope. It's eventually revealed that the reason he objects to their marriage is because the fiance is AMAB and had a sex change. After a moment of surprise, Kei and Yuri respond: "So what? That's so closed-minded!" and "In these days, one out of every ten people has had a sex change!"
  • Maho, one of the two main characters in the manga Double House, is a trans woman, as are a number of the secondary characters.
  • Family Compo has so many transgender and Crossdresser characters that it's hard to count. The main character's adoptive parents (both of them — that is, the dad is AFAB, the mom is AMAB), his adoptive father's assistants (all transgender, some post-op, some not), several dozen bit characters, and one of the character's love interests — his adoptive sister and cousin — may or may not be AMAB, given that about every 6 months she'd switch genders as she was growing up (It's never explained in the manga, although she's shown buying tampons at one point which strongly implies that she's AFAB.)
  • Fukakai na Boku no Subete Wo: Mei and Satori are both trans women and Mogumo is nonbinary. The manga starts with Mogumo dysphoric towards being identified as either male or female. They then join a cafe that helps learn them how to be comfortable being themself.
  • There is a LOT of debate on whether Nuriko of Fushigi Yuugi fits as a trans woman or as a Wholesome Crossdresser. It's best to thread VERY carefully around it.
  • Yayoi and her other female work colleagues in Futari Ecchi are trans women. They have a mostly decent portrayal: some characters such as the protagonists are generally amicable/respectful of her (occasional remarks aside) and the mangaka often includes information on trans women (such as their history in Japan, the different body types and what's considered acceptable and derogatory terms). One subplot in the series is Yayoi's relationship with Okahama: being the jerk he is, Okahama is disgusted when he first sees the pre-operative Yayoi's genitalia and has a "mental breakdown" over his attraction to her; although he takes a genuine interest her, he still refers to her as a man and often talks about her or their relationship in a derogatory way, leaving his progress to be a mixed bag.
  • A little known manga titled Gender Identity Disorder follows the life of a trans man. It begins with his childhood (telling his father he wants Santa to give him a penis for Christmas), and ends with him transitioned and leading a successful life, reconciling with his father before he dies.
  • Genkaku Picasso has Yosuke Hishida, who is explicitly described as suffering from Gender identity disorder. She puts on a good show of acting like a normal boy, so this causes some problems when [[spoiler:she's caught in the girls' bathroom. She's almost driven to suicide, but when Sugiura saves her and offers to listen to her troubles, Picasso (who has been inside the sketch of her heart) rallies the class to go to where she is and listen to her. When they do, they apologize for how they treated her and rally to let her wear the girls' uniform.
  • Gintama has some characters who are transgender, mostly trans women who belong to the okama club. Their portrayal is mostly unimpressive (the okama club members for example are very perverted and get frequently called monsters), but there are two standouts:
    • The widowed okama club leader Saigo has her own story where she has trouble raising her bullied son as a trans parent and said son (who's otherwise supportive) feels the need to prove that he's a man. After she saves his life, he gets the courage to invite her and everyone else in the club to parents' day and writes about how "beautiful" their hearts are.
    • Kubei is biologically female and was Raised as the Opposite Gender but does not consider themself to be either male or female. A whole arc is dedicated to this realization: the arc's antagonist questions Kyubei's feelings about their gender identity, and changes everyone's sexes as "punishment" for not abiding to gender roles. Despite having considered a sex change before, Kyubei finds little satisfaction in being male and eventually decides they are neither "manly nor womanly".
  • Commander Teral from God Sigma is literally a woman in a fairly masculine man's body. Ironically, she's the noble prince-type of the story despite being one of the main villains. She gets very little snark, which is pretty open-minded for an early '80s show.
  • The shoujo manga "Go! Go! Ichigo" is about a girl who falls for her old childhood friend who came back several years later as a girl.
  • Yoshiki Kitazawa from the manga Gravitation is an trans woman. In the first series, she's only had hormones to encourage breast growth but her lower half is still physically male. In the sequel, EX, she finishes her surgery on her lower half as well, like she's wanted to since she was 14-15 as stated in the fanbook.
  • Hanayome Wa Motodanshi is an educational, autobiographical manga about a Happily Married trans woman and her husband.
  • A chapter of the manga How I Became a Pokémon Card is about a trans boy named Akari. He lived as a boy all of his childhood, to the point where his best friend didn't know his sex, but has to now wear a female school uniform as he's entering middle school. He gets a Pikachu for his birthday, which he's mad about since it's not a "cool" Pokémon but a "cute" one. Akari eventually got over it and learned that it doesn't matter what a Pokémon looks like, that they all can be cool.
  • Alluka Zoldyck from Hunter × Hunter is probably a transgender girl. Her brother Killua, who is the only member of her family to treat her with any affection, refers to her as a girl, while her other brothers call her a boy, although her gender assigned at birth is not officially confirmed.
  • Celebrity stylist Nao from Ice Revolution, who forgives uber-Tomboy Masaki for destroying her favorite scissors, gives a makeover that makes her appear truly feminine "on camera" for the first time, and even leaves the fee for later. After The Reveal, Nao tells Masaki that they're Not So Different: both of them had a hyper-aggressive male Japanese Delinquent appearance that they're no longer comfortable with. Notably, she is the only person outside of Masaki's friends and family who can tell she's a girl at first sight.
    Masaki: How did you... know I'm a... girl...?
    Nao: Isn't it obvious?
    Masaki: (is completely mystified)
  • Criff/Cliff from Infinite Ryvius is a trans woman who transitioned a good time before the series started. You'd never know if it weren't for Word of God statements and a blink-and-you-will-miss-it line from her sister.
  • Christian of Innocents Shounen Juujigun is debatably a trans girl. It's a bit unclear if she's actually trans (or just using wanting to be a woman as an excuse to herself for loving a man), but considering the amount of emotional investment she shows to the idea of being a woman, it's most likely the former.
  • Mariandel from Ixion Saga DT is a trans woman.
  • Akira of Kanojo ni Naritai Kimi to Boku is a trans girl. The story revolves around her starting high school presenting as a girl, and her friends as they learn how to deal with the changes that come with her being out.
  • Kore wa Koi no Hanashi has Satomi, a woman who used to go to the same all boys' school as the protagonist, prior to her sex-change.
  • Kyou Kara Yonshimai is about a girl whose brother comes back from college living as a woman.
  • Mikihisa from Level E is a trans man and has felt male since he was four, and it turns out he's also intersex, with XY chromosomes. After much tribulation, the alien princess who's in love with him gives him a really high-tech sex reassignment.
  • Yuji from Liar Game is a trans woman. The Live-Action Adaptation made her a cis male, with a different design, who was originally Disguised in Drag.
  • Seiko, born and originally named Seishirou, from Lovely Complex. One chapter has her voice breaking which causes her to become depressed and she detransitions. The other characters try to convince her otherwise. She eventually transitions again after she goes to the hospital and gets a shot, which she says was for a cold that reversed her voice.
  • Kiyoharu from Mahou Shoujo Site is a 13 year old who recently began transitioning. Kids at her school bully her about being trans, which is what prompted the titular website to allow Kiyoharu to become a Magical Girl. Kiyoharu initially plans on getting revenge on her bullies using her powers, though this element is downplayed later.
  • Arisugawa "Alice" Kintarou from Maria-sama ga Miteru hates her masculine name and wishes she could have gone to an all-girls school instead of an all-boys school.
  • The third story in the one volume anthology manga Mascara Blues revolves around a trans girl who falls for a boy. She feels nervous about telling him about her "gender inversion" (as she calls it).
  • The Yuri anthology Mermaid Line has a Slice of Life story where a trans woman and her (apparently bisexual) fiancé decide what to do about her transition.
  • Kei from Moyashimon is a rare case of a character transitioning as the series occurs. She is introduced at the start, inexplicably disappears, and comes back later living as a woman. There's some ambiguity to her gender due to some lines implying she is cis, but she's overall considered trans by fans.
  • Izumi Nachi/Lady Nachi in Mugen Densetsu Takamagahara: Dream Saga is pre-operative in Nakatsukuni, and post-operative in Takamagahara. She takes full advantage of her female form, attempting to become the perfect girlfriend that she could never be in Nakatsukuni because of societal expectations... to a guy that didn't want her. The rest of Nachi's evolution goes from Clingy Jealous Girl to I Want My Beloved to Be Happy.
  • When introduced, Yena the Hyena of Murenase! Shiiton Gakuen is proclaiming himself a man's man while being drawn in the Little Bit Beastly style that the series uses exclusively for female characters instead of the Beast Man style of the males. This isn't him presenting as male, however. A quirk of hyena physiology is that females have an organ that resembles a penis and, until this is pointed out to him, the idea that he could be anything but male had legitimately never occurred to Yena. This prompts him to briefly try to be more feminine, even adopting female human Hitomi as a role model. When Hitomi's advice is to Be Yourself, Yena reasserts himself as male from that point onward. Yena's father and brother are accepting, only lamenting that the frilly clothing they got while Yena was trying to be feminine would go unused now.
  • My Hero Academia:
    • Tiger from the Wild Wild Pussycats team is stated in an omake to be a trans man who went to Thailand for sex reassignment surgery. A one-off gag mentioned how out of place a muscular man is among a group of Cat Girl-costumed heroes, but it's otherwise not taken into attention.
    • Minor villain Magne was also eventually confirmed to be a transgender woman.
    • 13 is nonbinarynote  and uses "they" pronouns in the English translation.
  • From Ludwig Kakumei, the Goose-Girl in the Well, Princess Julianna, whom we know for most of the series as Lui's "step-brother" Prince Julius. She very explicitly states that she doesn't identify as a man (or almost does before she cuts herself off), but everyone else seems to think of her as a crossdresser of some nature or another.
  • Isabella in Paradise Kiss is a post-operative trans girl who dresses in Elegant Gothic Lolita.
  • Pet Shop of Horrors:
    • One of the stories has Leon investigating the murder of who turned out to be a transgender man with a beautiful female alternate persona, who kept rooms of aquariums of transgender fish and a virtual pet of a beautiful female fish. She was killed by the bartender who had a crush on her when he found out.
    • In the Tokyo version, Count D and a friend visit a club for transvestites and trans women, all of whom are portrayed very sympathetically. The bartender/owner comments that they're just women looking for husbands and also makes reference to a place a floor up where men can meet other like-minded men. Count D is apparently on good terms with some of them and has tea with the group on a regular basis.
    • Tokyo has a rather tragic inversion, with a beautiful female model who was once a homosexual man. The sex change was done not because of gender identity but out of the mistaken belief that the guy he was in love with was straight and made himself the beautiful woman he felt his crush wanted and deserved. The crush, as it turns out, was a deeply-closeted homosexual and found the model's female body upsetting. The trans bartender comments that all the pain would have been avoided if the two had been able to be honest about their orientations.
  • Played with in Punchline. Yuuta was a boy who switched bodies with a girl ten years ago. He's been stuck that way since but the Second Law of Gender Bending didn't work out for him. He hates being a girl and still lives as a boy.
  • Felix Argyle from Re:Zero is confirmed to be a trans woman: she sees herself as a woman and prefers the name Ferris. Unfortunately changed in the 2016 anime adaptation where she's treated as a crossdressing male.
  • Sakura-chan and Amane-kun is a romance about two closeted transgender teens.
  • Akari in Samurai Deeper Kyo was raised as a woman to make her shamanic powers stronger, and it stuck. The series mostly ignores the implications of transgenderism (except as gag fodder) and makes her the strongest of Kyo's followers and, therefore, a complete badass.
  • Ren's sister in Sazanami Cherry is revealed to be transgender in the second to last chapter. Not even Ren knew because of their age gap. Ren only remembers her living as a girl.
  • Shimanami Tasogare:
    • From the same mangaka as Shounen Note, Shimanami Tasogare features Utsumi Natsuyoshi, a trans man who transitioned long before the start of the story. His focus chapters focus on him dealing with an old classmate who doesn't fully understand or respect his situation and deciding to stand up for himself, even knowing it may cause a rift between them.
    • Shimanami Tasogare also features Misora, a young boy who crossdresses in the safety of the drop-in center that the story centers around. While he dodges Tasuku's questions about his identity, it's heavily hinted that he has gender dysphoria and may be a closeted trans girl. Misora's case is still left ambiguous by the manga's end, focusing instead on him being able to express himself in the safety of the drop-in center.
  • Shounen Note has genderqueer characters, such as Yutaka's older sibling. The mangaka (who also made Nabari no Ou) is x-gender themself.
  • The class of 3C in Sket Dance meet the new board director's troubled son and The Voiceless Yuuki, who is eventually revealed to be biologically female while having "a heart of a boy". At that point, Yuuki had been bullied at school for this, and he stopped speaking as his voice would give his biological sex away. His father's concern is what lead to him trying to make Kaimei Academy stricter and separated by sex, as he believes expressing individuality will only get him bullied. The class does not react negatively, with Bossun saying that expressing individuality is a good thing and everyone will accept him for who he is.
  • Sorcerer Stabber Orphen has the local Cool Big Sis and Orphen's first travel partner, Stephanie. Orphen explains to Majik and Cleao that she used to be Stephan until few years ago, when she was seriously injured in a training accident and her body was horribly torn apart. During her recovery, she explained her situation to the local healers and asked them for sex change; they accepted, and she' much more happy and comfortable. Cleao and Majic are rather surprised when Orphen tells them (Cleao wonders if Stephanie's boyfriend and eventual husband Tim knows), but Orphen himself seems to be pretty nonchalant about the whole deal and it's never discussed again.
  • Hibari Oozora of Stop!! Hibari-kun! loudly voiced her disappointment in the fact that she doesn't have breasts and plans to eventually marry Kousaku. The anime avoids ever showing her naked chest despite the fact that she doesn't have anything to hide there. There's also a random island girl that looks almost exactly like Hibari (resulting in another Unsettling Gender Reveal moment for Kousaku and a girlfriend of Ibari's — one whom he doesn't know is trans.
  • Strange Mansion features a Stalker with a Crush who moves into the title apartment to be near her bishounen classmate. She discovers that her crush became a woman to be with her love interest (he was a bit disappointed that his first declaration of love came from a man but handled it calmly), which causes a Heroic BSoD. Of course, her wealthy conservative parents know nothing.
  • The BL light novel and anime Sukisho has transgender Team Mom Nanami.
  • Kaoru from Tamako Market is the sweet local florist voiced by Daisuke Ono. She's implied to be a trans woman.
  • Nathan Seymore of Tiger & Bunny is confirmed in supplementary sources to be agendered.
  • Tokyo Ghoul:
    • Tooru Mutsuki was born female, but was unable to reconcile his feelings of discomfort towards his gender. As such, he began living as a man.
    • Big Madam, a powerful female ghoul from the same series, was discovered to be biologically male after her death.
  • Hana in Tokyo Godfathers says, "I am a mistake made by God. In my heart, I am a woman."
  • The Trigun Maximum manga has Elendira the Crimsonnail, although she is presented as a transvestite. Vash is the only one who briefly recognizes her as female, and then only to insult her. She glared and said 'a woman like you' out of Wolfwood when he called her a guy one time. Apart from Meryl categorizing her as a transvestite (and complimenting her figure) after she falls out of the sky, it doesn't really come up otherwise; people are busy. The actual question is how everyone can tell by looking at her. It could be that she has a masculine voice, albeit very effeminate, which is quite common.
  • Played with in BC, aka. Commander Tenmei Uragasumi from Vandread, who is revealed to be a male agent who'd undergone gender reassignment to infiltrate the female pirate ship undercover. By the end of the series, he/she seems to have accepted living as a woman permanently.
  • Shuuichi Nitori (trans girl) and Yoshino Takatsuki (trans boy) from Wandering Son. Also their adult friend Yuki Yoshida (trans woman), who is implied to have had a full physical transition, as well as Nitori's classmate Makoto Ariga (trans girl) and Taiichirou Ebina (trans woman). In Takatsuki's case in particular, at least one character suggested that it wasn't so much that Takatsuki wanted to be male so much as they disliked being female. Their gender identity is left very ambiguous in the end.
  • In the manga adaption of Welcome to the N.H.K., one chapter has Yamazaki befriending a pre-op transgender woman, and even getting a job to pay for her operation. Unfortunately, this charity offends her, and she ends the friendship.
  • Aoi Futaba from You're Under Arrest!, one of the prettier woman officers in the Bokuto Station. ("She's girlier and cuter than all of us!") In an episode in the second season where she asks for help with a date with a man, Aoi says, "I have the body of a man, but the heart of a woman". Episode 6 explicitly mentions "transsexual".
  • One of the protagonists of Yuureitou, Tetsuo, is a transgender man. He killed his adopted mom after disputes about his gender two years prior to the manga. Despite this he's a pretty sympathetic if antiheroic character.
  • In Zombie Land Saga, it's revealed that Lily Hoshikawa, the Token Mini-Moe of the zombie idol group, was originally named Masao Go and assigned male at birth but identified as a girl from a very young age. The discovery that she was growing facial hair, along with the stress of overwork and her father seemingly caring more about her acting career than her, led her to die of mental shock. After the initial surprise wears off and Saki has had a good laugh over her extremely butch birth name, all of the girls quickly accommodate to the revelation once Lily firmly states that she's always going to be "Lily", while their manager plainly states he knew all along and rebukes the girls for thinking he might kick her off the group because of it. As for her father, he has proven to be largely accepting of her, although he mostly still calls her "Masao", which annoys her greatly.
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