Yaoi Manga with Trans Characters
Manga
Yaoi/Shounen-Ai/Boy's Love/BL manga with binary transgender, non-binary, and intersex characters. Some are headcanons- those are indicated by question marks. Also, some have a cis male/trans female relationship and shouldn't be labelled as BL.
Not on MAL (yet):
Ore ga Ryousei Nante Mitomenai!
Kiri (intersex boy) (protagonist)
Kiri's mother (intersex woman) (supporting)
Gentle Forest
Seowon Jung (intersex boy) (main)
Kuroe to Mesu no Sono
Sonogi (intersex boy) (protagonist)
Ryouseika Majiwaru Unmei no Tsugai
Aritoki (intersex man) (main)
Kalimeris Porno
Mimasaka (intersex man) (main)
Biting the Tiger
Naroo (non-binary) (supporting)
In a Heartbreak
Min Joo Lee (trans girl) (supporting)
Otogibanashi no Owarikata
Shizuku (trans woman) (supporting)
Not BL, but BL-adjacent:
30-sai de "Seibetsu ga, Nai!" to Hanmei shita Ore ga Around Fifty ni Natte Wakatta Koto.
Shou Arai (intersex man) (protagonist)
A (trans man and gay) (minor)
D (trans woman) (minor)
N (gender questioning) (minor)
T (trans man) (minor)
A-A'
Tacto (non-binary? and intersex) (main)
Hanshin (Suimu)
Lem Palmino (intersex man) (main)
Yuureitou
Taichi Amano (maybe genderfluid) (protagonist)
Tetsuo Sawamura (trans man) (main)
Simoun
Anubituf (trans man, gender-bending) (supporting)
Guragief (trans man, gender-bending) (supporting)
Devilman
Satan (intersex boy) (main)
Shimanami Tasogare
Dareka/Someone/Anonymous (agender) (supporting)
Natsuyoshi Utsumi (trans man) (supporting)
Misora (gender questioning) (supporting)
Murai-kun wa Mizuno-kun wo Dakitai
Shion Murai (trans boy) (protagonist)
Not on MAL (yet):
Ore ga Ryousei Nante Mitomenai!
Kiri (intersex boy) (protagonist)
Kiri's mother (intersex woman) (supporting)
Gentle Forest
Seowon Jung (intersex boy) (main)
Kuroe to Mesu no Sono
Sonogi (intersex boy) (protagonist)
Ryouseika Majiwaru Unmei no Tsugai
Aritoki (intersex man) (main)
Kalimeris Porno
Mimasaka (intersex man) (main)
Biting the Tiger
Naroo (non-binary) (supporting)
In a Heartbreak
Min Joo Lee (trans girl) (supporting)
Otogibanashi no Owarikata
Shizuku (trans woman) (supporting)
Not BL, but BL-adjacent:
30-sai de "Seibetsu ga, Nai!" to Hanmei shita Ore ga Around Fifty ni Natte Wakatta Koto.
Shou Arai (intersex man) (protagonist)
A (trans man and gay) (minor)
D (trans woman) (minor)
N (gender questioning) (minor)
T (trans man) (minor)
A-A'
Tacto (non-binary? and intersex) (main)
Hanshin (Suimu)
Lem Palmino (intersex man) (main)
Yuureitou
Taichi Amano (maybe genderfluid) (protagonist)
Tetsuo Sawamura (trans man) (main)
Simoun
Anubituf (trans man, gender-bending) (supporting)
Guragief (trans man, gender-bending) (supporting)
Devilman
Satan (intersex boy) (main)
Shimanami Tasogare
Dareka/Someone/Anonymous (agender) (supporting)
Natsuyoshi Utsumi (trans man) (supporting)
Misora (gender questioning) (supporting)
Murai-kun wa Mizuno-kun wo Dakitai
Shion Murai (trans boy) (protagonist)

Manga, 4 vol, 1991
Me:-
Author:-
Yuuji Ayukawa (intersex man) (protagonist)
Ookami no Hanayome
The Wolf's Bride

Manga, 5 vol, 2017
Me:-
Author:-
Louie Fridda (intersex man) (protagonist)
Boku no Ryouseiguyuu Syndrome
My Androgynous Syndrome

Manga, 1 vol, 2011
Me:-
Author:-
You/Yoh Yukino (intersex man) (main)
Liberty☆Liberty!
Liberty Liberty!

Manga, 1 vol, 2005
Me:-
Author:6
Kurumi Tokita (trans woman) (main)

Manga, 1 vol, 2004
Me:-
Author:6
Yumiko "Mary" (trans woman) (supporting)
Kyo "Sue" (trans woman) (supporting)
Kyo "Sue" (trans woman) (supporting)
Aa! Bocchama...!
Oh! My Mister...!

Manga, 1 vol, 2016
Me:-
Author:-
Neneko Shimonakazawa (trans woman) (supporting)

Manga, 1 vol, 2008
Me:-
Author:6
(Gomen ne, demo Aishiteru)
Mama (trans woman?) (supporting)
Mama (trans woman?) (supporting)
3-bansen no Campanella
While Being Seen Off by Campanella

Manga, 1 vol, 2017
Me:-
Author:7
Kodama (non-binary) (supporting)
Kaijuu ni Natta Gay
The Gay Who Turned Kaiju

Manga, 1 vol, 2017
Me:-
Author:7
Liam (trans man) (minor)
Uragiri wa Boku no Namae wo Shitteiru
The Betrayal Knows My Name

Manga, 13 vol, 2005
Me:-
Author:-
Elegy (genderfluid? and intersex)
Bokura no Chikyuu no Arukikata
Our Not-So-Lonely Planet Travel Guide

Manga, ? vol, 2019
Me:-
Author:-
Layla (trans woman) (supporting)

Manga, 1 vol, 2011
Me:-
Author:-
Kaoruku Someya (trans woman) (main)
(spin-off of Okane ga Nai)
(should not be labelled as BL)
(spin-off of Okane ga Nai)
(should not be labelled as BL)

Manga, 10 vol, 2012
Me:-
Author:8
Marika Aoki (trans girl) (protagonist)
(should not be labelled as BL)
(should not be labelled as BL)
Kono Koi ni Mirai wa Nai
There is no future in this love

Manga, 2 vol, 2016
Me:-
Author:7
Yuuji Manase (trans woman) (protagonist)
Kaoru (trans woman) (supporting)
(should not be labelled as BL)
Kaoru (trans woman) (supporting)
(should not be labelled as BL)

Manga, 2 vol, 2009
Me:-
Author:6
Nono Nosaka (trans girl) (main)
Nanako (trans man) (supporting)
(should not be labelled as BL)
Nanako (trans man) (supporting)
(should not be labelled as BL)

Manga, 1 vol, 2010
Me:-
Author:6
(Coyote Hita Hita Hita Kousagi Niya Niya Niya Watashitachi Fura Fura Fura Anata dake Niya Niya Niya/The Coyote Quick. The Bunny Grins. We Stagger. We are the Only One Smiling)
Makiko Tabuchi (trans woman?) (main)
(should not be labelled as BL)
Makiko Tabuchi (trans woman?) (main)
(should not be labelled as BL)

Manga, 1 vol, 2009
Me:-
Author:6
(Yume wa Yoru Biraku/Dreams Unfold at Night)
Tone (trans woman) (protagonist)
Salon Customer (trans woman) (supporting)
(should not be labelled as BL)
Tone (trans woman) (protagonist)
Salon Customer (trans woman) (supporting)
(should not be labelled as BL)
Nobara
Wild Rose

Manga, 1 vol, 2010
Me:-
Author:7
(Mimi-kun no Boy no Kisetsu/Mimi's Boy Season, Mimi-kun no Heart no Earrings/Mimi's Heart Earrings)
Mimi Mita (trans woman?) (protagonist)
(should not be labelled as BL?)
Mimi Mita (trans woman?) (protagonist)
(should not be labelled as BL?)

Manga, 1 vol, 2010
Me:-
Author:6
Ren Takano (trans girl?) (main)
Umi Takano (trans woman?) (supporting)
(should not be labelled as BL?)
Umi Takano (trans woman?) (supporting)
(should not be labelled as BL?)