Trans Anime (Transforming gender works, too)

Hourou Musuko, aka Wandering Son, immediately springs to mind. It's a slice-of-life series about a group of kids entering middle school and coming to terms with their gender and, to a lesser extent, sexual/romantic orientation. The protagonist is a trans* girl.

Kino's Journey arguably counts, based on what I've heard. The protagonist is AFAB, but they use male first-person pronouns and present in a gender neutral way. Reading them as not cis would be reasonable.

 

Kashimashi is really good. It's about a boy who is killed by aliens, then brought back to life as a woman.
Strawberry Eggs is also kinda that sorta thing. It's about a teacher who tries to get a job, but the position is for a woman. so he ends up crossdressing (with the help of his psycho landlady) to get the job.

 

I liked Simoun. It's a mecha yuri series where everyone is born a girl and decides their gender when they're 17.
I also liked No Bra, but I'm not really sure if that counts as trans anime.

 

well its not anime but there is an AMAZING Japanese drama that went on for 12 episodes called I.S. (inter sexual). it follows a family who give birth to a child who is I.S.; he (im calling him he because that's how he mostly saw himself, though he is played by an actress) is born with both male and female anatomy, and the family are urged to decide what sex they want the child to be so they can start hormone treatment and surgery. However the family cant bring themselves to do it for fear that they would trap their child in a body he/she does not feel comfortable in and decide to let him make the decision when he is legally old enough. thats the first 15 minutes of an hour long episode, i strongly recomend watching it, even if its just the first episode its really powerful and emotional.
by the second episode he is starting highschool but his hormone's are starting to produce more estrogen which are making him seem much more feminine than masculine, so the school say they will only take him on board if he agrees to come dressed and act as a girl. because the school has really good education he agree's, and i wont say anymore. i stopped watching around episode 8 because the subs were taking to long and i completely forgot until now. up until that point it was amazing, never seen any drama tackle this kind of thing.
if you watch it please let me know what you think.

 

if you cant find it try the full title, they have it on dailymotion

IS ～Otoko Demo Onna Demo Nai Sei～