There's a children's book named 10000 Dresses, by Marcus Ewert and Rex Ray, about a young trans girl who wants to wear dresses but isn't accepted by her parents.
In Brian Katcher's Almost Perfect, the main character meets, and falls in love with the new girl, who happens to be a trans girl. He struggles to accept her, and eventually does so, based in part on the author's interviews with young transgender people.
The Art of Being Normal is about a closeted fourteen-year-old trans girl who befriends the new boy at her school who also turns out to be trans (albeit, already out and going stealth).
Nnedi Okorafor's Binti: Haifa cheerfully explains that she's a transgender woman who medically transitioned when she was thirteen. The sci-fi setting has its fair share of human (and alien) prejudice in other areas, but no one bats an eye at this; Binti admires her for having known herself and gotten what she wanted.
Blackfish City by Sam J. Miller. One of the main characters is Soq, a gender-neutral street kid working as a messenger for the underworld. Unlike most examples, this has little relevance to the plot, simply being an aspect of Soq's character.
A character in Tamora Pierce's book Bloodhound is a trans woman called Okha/Amber. In that world, it's apparently referred to as being 'tapped in the womb by the Trickster God'.
The Bone Palace by Amanda Downum has Savedra Severos, the transgender mistress of the Crown Prince, as its second viewpoint character. Transgender people are only marginally accepted in this culture; they have a long history in the open, but most hijra (the "third sex", encompassing all varieties of transgender and agender people) live apart in the company of their own. Most are either in the priesthood or are mystics and fortune-tellers. Savedra is lucky; she was born wealthy and her mother and family members accept her. Despite the magic of the setting, nothing seems to give any kind of Easy Sex Change; Savedra at one point laments her Adam's apple and her small breasts, and she retains functional male genitalia, so physical sex reassignment does not appear to be possible.
Neil Gaiman's short story Changes concerns the accidental creation of a drug that allows an Easy Sex Change and the ramifications of said drug on the global society. Gender identities are blurred as the drug takes on a recreational use, and in the end (as with every conflict of generations) it's seen as something ordinary (if mildly dirty) by the young and disgusting by the old.
The novelette Cinder Ella by S. T. Lynn is a retelling of Cinderella in which the titular character is a trans woman whose stepmother and sisters force her to present as male and use her dead name. The princess meets her in this guise but has no complaints about her showing up to the ball in a dress and recognizes her immediately.
Curiouser: The protagonist Aidan Frost is a trans woman. An abusive female lover tries to torment her by forbidding hormone replacement therapy and forcing her to keep her hair short, but unusually for this trope Aidan has no problems accepting her anatomy, and is naturally androgynous.
The novel by David Ebershoff called The Danish Girl is a fictionalized account of the first widely publicized gender reassignment surgery ever performed. The subject of the novel, Einar Wegener, begins to confront his body and gender issues after being asked by his wife to pose in a dress so that she may finish a commissioned portrait of a friend of the young couple. Einar is then moved by this experience to begin identifying herself as Lili. The novel explores the situations of both Lili and the ever-loving and supportive Greta as they come to terms with Lili's transformation. A film adaptation starring Eddie Redmayne as Lili and Alicia Vikander was released in 2015.
Each Little Universe character Jack Derrida is, as they explain to new acquaintance Ziggy when they're introduced, 'not boy Jack, but not girl Jack either, just to get that out of the way'. Ziggy finds this easy to accept (simply 'person Jack'), which Derrida seems to find pleasantly surprising.
Earth's Children: Though it's not explicit of course, several characters appear to be what we'd now call transgender or non-binary. Socially they're accepted in their cultures, even considered very attractive, and expected to become shamans. There's mention of one Mamutoi who's biologically male but identifies as a woman so strongly as to experience sympathetic pregnancy, plus dressing in female clothing.
Though never stated out-right, Veronica from Eden Green is transgender; she transitioned as a teenager, causing some tension with best friend Eden.
Coydt Van Haaz, the women-hating Big Bad of Jack Chalker's Empires of Flux & Anchor, turns out to have a very tragic Back Story. He was castrated and then given an involuntary (and irreversible) Gender Bender as a teen. He wants his manhood back and he wants it bad. Since that's not possible he wants to make all women suffer for what happened to him. This is very unusual in a 'verse where Easy Sex Changes are canon.
F2M: The Boy Within by Hazel Edwards and Ryan Kennedy is about a teenage trans boy named Finn. He's also a part of a punk rock band called "Chronic Cramps".
Tonkee in The Fifth Season is transgender, which is only presented as an issue when she's living rough for a while and runs out of her hormone medication. In her past as Binof, her coming out caused friction with her family due to it disrupting their plans for her Arranged Marriage.
Form and Void features not just one, but TWO transgender protagonists (makes sense, given that both authors are trans themselves). One of them, Caren, is a trans woman and foul-mouthed mage hunter. The other, Ash, is a stoic trans masculine alchemist. Together, They Fight Crime!.
The Four Profound Weaves: The desert cultures accept transgender people as "changers", including non-binary "in-betweeners", and have near-universal access to Gender Bender magic through the first of the titular Weaves. Uiziya, one of the protagonists, is an elderly trans woman who transitioned as a young child and never looked back; the other protagonist is a nameless trans man who grew up in the much more prejudiced city of Iyar, was Late Coming Out, and is still adjusting.
George by Alex Gino is about a 10-year-old closeted trans girl who wants to play Charlotte in her school's play adaptation of Charlotte's Web.
The comic neo-noir Get Blank features Lara Hernandez, a minor but helpful character who is a member of the Golden Dawn and has contacts in law enforcement. Her gender (and expression) isn't a plot point.
David Thomas's Girl is about Bradley, a macho, working-class, rugby-playing young man who accidentally goes through sexual reassignment surgery (and simultaneous breast augmentation) through a hospital error. It is actually quite sensitive and sweet, even if it is a bit of a stretch that the (almost stereotypically) blokish Bradley decides to commit himself to become a woman so quickly, ending up as a sweet-natured, pretty (thanks to hormones and plastic surgery) and content young woman named Jackie.
In the German novel Gottes Bodenpersonal, the sex worker Loreen is violently attacked by a john who discovers her/his penis while he sexually assaults her/him. When not working, Loreen identifies as male and goes by the rather androgynous name "Lauren". Lauren says he feels okay in his male body but really feels female in Loreen's clothes and make-up. The term "genderfluid" is not used, though. Later events hint that the trans identity issue was caused by childhood sexual abuse, and Lauren is most comfortable as a gay man.
The Hearts We Sold has Riley, a trans girl. Her parents threw her out for it, and it's implied that she made a deal with the Daemon in exchange for a sex-change operation, or possibly hormones.
The Heaven Cycle has, as the main characters, Tango and Mint, who are biologically female but who identify to neither gender, and the story uses the pronouns 'they' for them.
In Heroin Story, one of David's college friends is a trans man.
Roxy comes out as nonbinary in the Meat epilogue of The Homestuck Epilogues and uses he/him pronouns. In the Candy epilogue, they question their gender a few times but ultimately continue to identify as female. Calliope also comes out as nonbinary in the Meat epilogue.
The title character from I Am J by Cris Beam, a Jewish, Puerto Rican, trans boy teenager who is deeply insulted by being called a lesbian, or even by his confused parents calling him "my daughter".
In Seanan McGuire's Indexing series, main character Henry's twin brother appeared to be her twin sister at birth. Being transgender actually prevented them from falling into a Snow White Rose Red narrative, although Henry is still a Snow White.
Lily and Dunkin is about a teenage trans girl and a boy with Bipolar Disorder who become friends.
Luna by Julie Anne Peters is about a trans girl's teenage sister Regan, who often has to lend Luna clothes or cover up for her because their parents do not know.
Non-binary identities are a matter of course in the Hexarchate; "alt" characters like Meng and Zehun are referred to by "they".
Transgender identities are similarly accepted, including medical Gender Bender options, with only some slight conservatism in the Kel faction due to seeing body modifications as an affectation of their rival Andan faction. Kel Brezan is a trans man who did not opt for medical transition and is respected by his peers despite that conservatism; Andan Tseya is a special ops agent and a trans woman who socially and medically transitioned years before the time of the books.
Istradez is an unusual case, having been voluntarily modified into a maleform for a Body Double job. He now uses male pronouns, but per Word of God, Istradez's attitude towards gender is "whatevs".
Danny Tozer, the protagonist of the Nemesis Series, is a transgender woman whose body instantly transitioned when she gained her superpowers. The same series also features the non-binary Kinetiq in the second book.
Imogen Binnie's Nevada is renowned for being one of the first novels that focuses on a trans character's life years after they've transitioned. The main character, Maria Griffiths, is a trans woman who, after running into trouble in her personal and professional life, decides to take a road trip to Nevada on a whim.
Michelle Cliff's No Telephone to Heaven has the trans/genderqueer character Harry/Harriet (also known as H/H), who is AMAB and identifies as a blend of male and female. At the beginning of the novel, s/he has a masculine appearance, wears bikinis, puts on feminine make-up, and occasionally dresses in the genderfuck style (for example with both a tuxedo and very campy make-up. Hilarity Ensues as this impish black Jamaican character passes for an African man to fool an American tourist, who really thinks he has just met "King Badnigga of Benin!"). Towards the end of the novel, H/H starts living and presumably identifying as Harriet, a white nurse, which involves double 'passing'. H/H is very aware that even as 'she' is respected as a generous nurse, s/he could literally get lynched for being trans and for passing for white, but makes this choice because a black man couldn't become a nurse. This character plays a huge role in the development of the very confused main character Clare Savage, a white-looking middle-class mixed-race Jamaican woman who questions the racist standards of her formerly slave-owning family and might further be bisexual. His/her ability to transcend social binaries and to fool racists and homophobes/transphobes is part of his/her attributes as a Trickster figure.
In the second book of the Outlander Leander series, Valli is a trans man. Notably, he wears dresses and is considered beautiful, but these traits aren't considered feminine in their culture. Valli is accepted as a man without question.
The Pants Project is about a trans boy trying to change his school's dress code policy that requires boys to wear pants and girls to wear skirts.
Parrotfish by Ellen Wittlinger is about a trans boy, Grady Katz-McNair. At the beginning of the book, Grady decides he wants to officially come out and change his name from Angela to Grady. The title of the book comes from his nerdy friend, who points out that female parrotfish often change to males.
Angela Carter's The Passion of New Eve (1977) is a novel about a British man, Evelyn, who is, well, castrated by Straw Feminists and made into "a New Eve". It's a satire on Feminism in general, Freudianism, and all other sorts of things. Also features a Dystopic America in the process of caving in on itself.
Paternum is a web novel about a non-binary superhero named Quinn. Quinn is a college student who finds an experimental supersuit that their mother, who has been missing for 15 years, invented before vanishing. The same series also includes Holly, a genderfluid superhero who presents as female in her civilian life and as male when he's being a hero.
In an odd twist, Gurgeh (from The Player of Games by Iain M. Banks) is regarded as being a bit odd because, although changing sex is the norm for most (human) citizens of the Culture, he has never done so. The strong implication is that Gurgeh regards everything as a game and at some level regards being a receptive sexual partner as losing. At the start of the book, it's mentioned that a distinct majority (six in ten?) of his ex-lovers have become, and stayed, FtM.
Ann Leckie's The Raven Tower: The protagonist Eolo is a young trans man in a fantasy nation that doesn't legally acknowledge his identity, so he left home and only discusses the topic with a few trusted people. He has mixed feelings about a proposition of a magical sex change and rebuffs the offerer for being intrusive.
Mawat: [The Raven] could make it so you could... so you could be who you are. Eolo: I already am who I am.
The title character in The Saga of Tuck is a teenager who is physically intersexed, and (possibly) bi-gender. A number of minor characters are also transgender, and several more are Transvestites.
Seawalkers: This children's series features a trans man named Johnny. He's the uncle of the main character Tiago and basically raised him.
David Nobbs's Sex and Other Changes is about a transgender married couple, both of whom transition in the course of the novel.
Zoe Marriott's Shadows on the Moon has Akira, a trans woman. When she became the Shadow Bride she should have been killed when this was revealed, but the prince understood and described her as having a female heart.
Attempted as a Defied Trope in The Silence of the Lambs when the police contact a gender transition clinic trying to find a lead on serial killer Buffalo Bill. The police have to explain that they're not looking for a trans woman, but a mentally-disturbed man who mistakenly believed he was a trans woman. Based on real-life serial killer Ed Gein, who was actually obsessed with cannibalism, but was portrayed by the media as such. Both this, and the reasoning used still being based on harmful stereotypes and outdated medicalised ideas of trans people mean this plot point remains one of the most commonly cited examples of transphobia in literature (not helped by the fact that The Movie even leaves that explanation out).
Alanna has always defied labels. She took the best bits of being a woman and a man, and created her own unique identity. I think the term is 'gender-fluid', though there wasn't a word for this (to my knowledge) when I was writing her.
Steel Crow Saga: Kosuke is a trans man who transitioned sometime during his years apart from his childhood friend Jimuro, a viewpoint character. They happily resume their relationship, romantic subtext included; both Jimuro's dialogue and narration use Kosuke's new name exclusively, including in Flashback scenes.
In Maria V. Snyder's Study trilogy, it turns out Commander Ambrose has both a female and male personality within an AFAB body due to magic — his mother died giving birth to him and her spirit entered his body (and apparently changed his genitalia). The female personality is allowed out whenever the Commander leaves the country and is officially an ambassador.
Stranger Than Fanfiction has Samantha Gibson, who grew up feeling like she was meant to be a boy, and wants to get a gender reassignment operation. Part of the conflict regarding this is telling her friend Topher, who has a crush on her, and worrying how he might react to it.
Symptoms of Being Human is about a genderfluid teen named Riley who has a blog about being nonbinary. After their blog goes viral, someone at their school connects the blog to them and threatens to out them.
Anna Madrigal from Armistead Maupin's Tales of the City and its sequels, along with the television mini-series adaptations.
A very casual mention in Becky Chambers' To Be Taught If Fortunate. The astronauts wear enzyme patches which allow their bodies to adapt to conditions in space and on alien planets, for example by letting them absorb radiation as food. The narrator off-handedly mentions that they are used widely on Earth for medical functions and that fellow crew member Jack wears one to produce the testosterone needed for what he calls his 'second puberty.'
Tales of MU features Steff, a trans female half-elf. In addition, the culture of the subterranean elves features an "ornamental" third gender of trans women called "halfkind," who undergo a magical transformation that enhances both breasts and penis/scrotum, and who serve mostly as a status symbol for their families. Steff eventually is given the halfkind potion by a subterranean friend.
An Unkindness of Ghosts: Theo's gender identity is ambiguous even to him, since his rigid, dogmatic society doesn't acknowledge transgender identities. However, he deliberately avoids some elements of masculine gender expression, secretly takes testosterone blockers, and outright tells a close confidant that he's not a man.
Revealed to be the case for The Princess in Velveteen vs. via origin story.
In A Civil Campaign, the dashing and unconventional Lady Donna Vorrutyer undergoes gender reassignment at age 40 to become Lord Dono. As this is SF, Lord Dono's transformation is perfect — he's even fertile. Lady Donna chooses this course so that she can prevent a corrupt male relative from inheriting her dead brother's countship and its attendant responsibilities. Barrayaran law doesn't allow women to inherit countships, but neither is it exactly set up to deal with transgender people — in the end Dono prevails. And ends up engaged to be married. One assumes Donna was originally bisexual.
Elsewhere in the Vorkosigan series, it's stated that people who choose to have their brains transferred to younger clones often choose to change sex when they do.
Generator (Jade Sinclair, nee Jared Reilley) of the Whateley Universe. Aside from this relatively realistic instance, a major part of the series that transgender mutants with the Exemplar trait (such as Chaka) will almost always get the Gender Bender change they want due to the power's 'ideal self' aspects. A number of other transgender mutants who don't possess this trait find other ways to change their sex, whether through 'sticky' powers such as ectoplasm manifestation or PK shells (Beltane, Mega-Girl), Applied Phlebotinum (Delta Spike), or Functional Magic (Scapegrace). Of course, those who are subject to unwilling gender bending, such as Phase, Jobe Wilkins, or Hat Trick, in effect become transgender regarding their former sex.
There's a children's book called When Kathy is Keith by Dr. Wallace Wong, who works with transgender youth. It's about a trans boy named Kathy who no one believes is really a boy.
In the young adult novel Where No One Knows, main character Kellan, a 16-year-old transgender boy, travels across the country to find a new home after his mother kicks him out—for having psychic powers.
Cam of The Witchlands is biologically female, but prefers to be treated as male and can, understandably, get rather agitated when people don't take this seriously. Whether Cam is actually transgender is never really spelled out loud, but the implication is clear. Considering Merik's reaction (he finds it rather odd but decides to roll with it), this doesn't seem very common in the Witchlands.
Also, Muldoon hires a transgender friend to housesit for Garp's son after he was in a bad motorcycle accident. The two eventually get married.
Worm has Circus, a minor supervillain who appears male in civilian identity and female in their costumed one. Even Tattletale isn't entirely sure which gender Circus identifies as, which is presumably their intention.