Haikei, Sekensama.
Dear, the World.

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word soup for search results: trans man, trans men, ftm, transmascs, nonbinary, ftx, transgender

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)

some of the manga have aroace characters too

I have not read everything in here! Some might be wrong.

Mangas with transgender authors and/or illustrators. Not all the mangas have transgender themes in them.

Part 2: https://myanimelist.net/stacks/54374


Not on MAL (yet):

Ayana Tsubaki (trans woman) (author)
Watashi, Danshikou Shusshin Desu. Comic

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

Keito Gaku (trans man) (author and illustrator)
Akarui

Chii (trans woman) (author and illustrator)
Majo ni Naritai Otoko no Ko
Manga de Wakaru: Taino SRS (Seitenkan・Seibetsu Tekigou Shujutsu)
Mofu☆Mofu: Ichigo Aji (that one's on MAL- I just can't add it for some reason)

Trans shojo-chan (trans woman) (author and illustrator)
Mirai kara kita Jibun ni Onna ni naru you Settaku Sarersu Hanashi
Danshi Jidai no mtf no Manga/Koukousei Hen

Asuka Miyazaki (x-gender) (author and illustrator)
Kyouhaku sei Shougai desu!
Kyouhaku sei Shougai Chiryou Nikki

Shou Arai (intersex man) (author and illustrator)
"Seibetsu ga, Nai!" Hito-tachi no Hoken Taiiku
Anokoro Ore wa Joshikousei
Asia wo Futari de Aruite Mita - Chuusei Oji-san to Otokonoko no Ryokouki
Chuusei Furo e Youkoso!
Ore no Mawari no "Seibetsu ga, Nai!" Hitotachi - Arai Shou no Sekumai Kouyuuroku
Saikin sa Otona to Wakamono ga sa... Suggoi Chigaku ne!?
Seibetsu ga, Nai!
Seibetsu R!
Seibetsu x Renai Hakusho

Kazuki (x-gender) (author)
Onna no Karada ga Iya nano de Mune wo Torimashita

Poppy Pesuyama/Stunning Sawamura (x-gender) (author and illustrator)
Sasada wa Tomodachi

More manga featuring LGBT (gay, lesbian, bisexual, binary transgender, non-binary, genderqueer, intersex, queer, pansexual, asexual, aromantic, etc.) characters in non-BL/non-GL manga.

Part 1: https://myanimelist.net/stacks/37019


Not on MAL (yet):

"Onna" to shite Idakaretai...Seitenkan shite, Hatsukoi wo Mou Ichido.
Sanae Takahashi (trans woman) (protagonist)
Machiko (trans woman) (supporting)

Akarui
Maki Sanada (trans boy) (protagonist)

Chiguharu
Tooru/Tohru (trans man) (protagonist)
Yuki (trans woman) (main)

Gay Fuuzoku no H Jijou
Kazuaki (gay) (protagonist)
Nori (gay) (main)

Girlfriend
Megumi Makimura (bi) (protagonist)
Kaoru Shirasaki (trans woman) (main)

Itsuka Shinu Shoujo
Yuuki Akai (trans girl and lesbian?) (main)

Kamisama, Boku wo Koroshite Kudasai - Otoko no Karada de Umareta Jigoku
Subaru Kawase (trans girl) (protoagonist)

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

Otto wa Jitsu wa Josei Deshita
Tsushima Tsushima (pan) (protagonist)
Wafuko Tsushima (trans woman and queer) (main)

Sayonara Chinchin Welcome Manman ~OL ni Naritakute Seibetsu Tekigo Shujutsu shimashita~
Yoriko "Yoripi" Kamikawa (trans woman and lesbian)

Queer mangas by queer mangakas for a queer audience. I didn't include memoirs/biographies for this list (I did make another list for it already: https://myanimelist.net/stacks/28845 )

Not on Mal (yet)

Akarui
Keito Gaku (trans man) (author and illustrator)
Maki Sanada (trans boy) (protagonist)

Majo ni Naritai Otoko no Ko
Chii (trans woman) (author and illustrator)
Koto (trans girl) (protagonist)

Mirai kara kita Jibun ni Onna ni naru you Settaku Sarersu Hanashi
Trans shojo-chan (trans woman) (author and illustrator)
Yuuka (trans woman) (protagonist)

Danshi Jidai no mtf no Manga/Koukousei Hen
Trans shojo-chan (trans woman) (author and illustrator)
Natsuki (trans girl) (protagonist)

Born This Way
Mieri Hiranishi (lesbian) (author and illustrator)
Nameless Protagonist (lesbian) (protagonist)
Kanade (lesbian) (main)

More trans characters from fan-translated manga. Organized roughly by year.

(My definition of a trans manga is one that has a main trans character. Them being transgender may or may not be a big impact on the story.)

Part 1: https://myanimelist.net/stacks/55094