Shoujo Bigaku
Girls' Aesthetics

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Manga that feature transgender boys/men.

Part 2: https://myanimelist.net/stacks/37834


Not on MAL yet:

Akarui
Maki Sanada (trans boy) (protagonist)

Oppai wo Totta Kareshi
Haruka Naruse (trans boy) (main)

Sakura-chan to Amane-kun
Amane (trans boy) (main)

Uchi no Danna ga Kawai sugiru ~tsu! Moto ♀ no Ikemen Nyuuseki Shimashita!!
Husband (trans man) (main)

Chiguhagu
Tooru/Tohru (trans man) (protagonist)

Seishun Minority
Sera (trans boy) (main)

Bokura no VR
Miharu Akina (trans boy) (main)

Ore no Karada wa Nande Onna Nanda?
Ryuutarou "Ryuu" Suzumiya (trans man) (protagonist)

Yuri/Shoujo-Ai/Girl's Love/GL Manga with binary transgender, non-binary, and intersex characters. Some of them feature a cis female/trans male relationship and shouldn't be labelled as GL.


Not on MAL (yet):

Josei ga Suki na Josei to Otoko datta Josei no Hanashi
Makoto (trans woman) (main)

Osananajimi Yuri (?)
College Girl (trans woman) (main)

Otto wa Jitsu wa Josei Deshita
Wafuko (trans woman) (main)

Sayonara Chinchin Welcome Manman ~OL ni naritakute Seibetsu Tekigou Shujutsu shita~
Yoriko Kamikawa (trans woman) (protagonist)

Girlfriend
Kaoru Shirasaki (trans woman) (main)


Not considered GL, but GL-adjacent:

Umareru Seibetsu wo Machigaeta!
Mafuyu Konishi (trans woman)

Seibetsu X
Asuka Miyazaki (x-gender)

Hourou Musuko
Shuuichi Nitori (trans girl)

Kyou kara Yonshimai
Kashiwa Manabe (trans woman)

Densen Complex (Love Horizon)
Yuko Matsuno (trans woman)

Kaoru-san no Kikyou (Senpai)
Shirafuji (trans woman)

Devilman Lady
Asuka Lan (intersex girl)

Kanojo ni Naru Hi: Another
Aya Kurokawa (male to female)

Kanojo ni Naritai Kimi to Boku
Akira Yonezawa (trans girl)

Shoujo Kakumei Utena
Utena Tenjou (genderqueer?)

All Manga (that I could find on MAL) from the Japanese magazine Yuri Shimai (2003-2004).
Contains Yuri/GL works from multiple authors.
Precursor to Comic Yuri Hime.
Only Manga and One-shots are included.

*Label if applicable: (Magazine volume number).(Order in volume). (Name of one-shot or chapter count)