Alice's Adventures in Wonderland
- Magical Metamorposis is about a transgender Harry Potter, who eventually chooses the name Holly. It is very in depth and accurate about the trans experience, though with added fantastical elements.
- In Formerly Known as Harry Potter?, Harry is taken in by Social Services at age four. She transitions as Lily by age five and is adopted by the Grangers, being raised as Hermione's sister.
The Fairly Oddparents
- Trans Girl Timmy Turner is an AU comic where Timmy reunites with Trixie as adults and comes out to her as a trans woman.
- I Wish is a oneshot based on how Timmy met his fairy godparents. In it, Timmy is a trans boy (and Cosmo is trans too, explaining his pregnancy). Cosmo and Wanda already knew his preferred name before being told.
Land of Oz
- Due to being Raised as the Opposite Gender and initially not wanting to transform back into a girl, it's common to depict Princess Ozma as either a trans boy or as nonbinary. One example is The Gender Ninja of Oz, a oneshot where Ozma feels uncomfortable being either female or male, so they uses the Magic Belt to turn themself more androgynous.
- Lightning is a Dorothy/Tip oneshot where Tip refused to be turned back into a female and decided to stay as Tip.
The Legend of Zelda
Life Is Strange
- Bloom re-imagines Max Caulfield as a trans girl who recently started taking hormones.
My Little Pony: Friendship Is Magic
- The Bright Side Of The Moon is a fic where Luna comes out as a trans stallion after repressing it for a millennium.
- Lopoddity: Sweetie Belle and Rumble's daughter Prima Donna is a trans filly who came out at a young age.
- Pandemic features multiple trans characters in the side stories, most prominently Tonya and Phobia.
- Trans Ponies is an unfinished comic where Rainbow Dash leaves to get a magic procedure done that will transition him into a stallion.
The Penguins of Madagascar
- Neverland is a 400-word story that reinterprets Peter Pan as a trans boy who rescues trans children.
- Pokémon Reset Bloodlines reveals that Melissa is a trans woman. This is a nod to how her anime counterpart was male in the original Japanese, but was dubbed as female.
- Celadon's New Blossom is a story about how Ash is Disguised in Drag after he becomes Erika's student. He is a cisgender crossdresser, but to go along with the guise his ID is changed for simplicity's sake. A Pokémon League investigator comes to inquire on the change and comes to the conclusion that Ash is transgender. Ash is too stunned to deny her. In the end, Erika and Ash both conclude that maybe people thinking he's a trans girl will make things easier for now. It'll be trouble when he eventually goes back to Ash, but for now Ash uses being trans as cover-up for whenever people learn that he's male.
- Denounce The Evils:
- Harley is a trans woman who has dealt with the media's transphobia after coming out.
- James had always thought he was Camp Gay until he's reunited with Harley. He figures he has an Ambiguous Gender Identity and goes to Harley for help. It's implied that James might be genderfluid.
- Yamujiburo: One of James and Jessie's kids, Jean, is non-binary.
- The oneshot The Beauty In Ugliness turns Gladion into Lillie's identical twin and a trans boy. He faced abuse by his mother Lusamine, which led to him eventually running away from home.
- RWBY: Scars:
- In the RWBY rewrite RWBY: Scars, Ruby is a trans girl who began hormones prior to the story. She comes out to her teammates Weiss and Blake in chapter 20 after her girlfriend Penny comes out about being an android. Penny's troubles and desire to be thought of as a "real girl" resonated with Ruby to the point of causing her to tear up and out herself.
- Jaune is a transgender boy. He transitioned right before coming to Beacon. He cut off his ponytail, stole his grandfather's sword, and ran off without telling his family.
- After being dragged back home by their father, Weiss notices that her twin Whitley has transitioned. Whitley keeps his Gender-Blender Name even after transitioning.
- Yang in the Alternate Universe Fic White Noise is a trans woman. Her dysphoria plays a huge role in her relationship with others, especially her Love Interest Weiss.
- The Real Weiss Schnee revolves around Weiss coming out as a trans man after he's forced to go in disguise.
- #Trans Stuff is a oneshot where Jaune is nervous about telling his girlfriend Pyrrha that he's transgender. As it turns out, not only is Pyrrha herself trans too but she was in a celebrity ad campaign for trans youth a few years back. Ruby is also trans in the oneshot and is the first person Jaune came out to besides his family.
Sonic the Hedgehog
- In We Are The Chatroom Gems, Smoky Quartz is Agender, implied AFAB.
- Momentum has "Genderfluid Amethyst" as an actual tag.
- Portraying Pearl as transgender is also a minor trend, as you can see here.
- The Warriors fic Little Fires is about a tortoiseshell OC who is a transgender she-cat. Considering how tortie toms work, Emberpaw has heavy implications of being intersex as well.
- Warriors Rewrite:
- Firestar is changed from a cisgender tom instead a transgender tom. He transitioned as a kit.
- To explain how he's a tortie tom, Redtail is a transgender tomcat.
- Blood! Rusty AU:
- The AU contains a few transgender cats, such as Ruth and Brick.
- Dusk comes out to Rusty as non-binary, with their seemingly mean attitude coming from trying too hard to emulate mollies in the Clan.
- In Warriors: The Power of Three (Rewrite/AU), Mothwing is transgender. She and Leafpool had a Forbidden Love and had the Three together.