Andoroid wa Furimukanai

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Some manga that features a non-binary/x-gender character. Some are headcanons- those are indicated by question marks.

Part 2: https://myanimelist.net/stacks/37987
Part 3: https://myanimelist.net/stacks/55436


Extra non-binary manga that's not on MAL (yet):

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

Then I saw RuPaul's Drag Race': coming out as X-gender in Tokyo
M. A. Joy (x-gender) (protagonist)

Kyouhaku sei Shougai desu!
Asuka Miyazaki (x-gender) (protagonist)

Kyouhaku sei Shougai Chiryou Nikki
Asuka Miyazaki (x-gender) (protagonist)

Unknown Color
Chiaki Hinaga (non-binary) (protagonist)

Quintet×Question
Mokuba Ao (x-gender) (main)

Bloody Chinatown
Kanaya (gender-free) (main)

Bara Shishaku
Gideon (genderless/gender ambiguous?) (main)

Yuri/Shoujo-Ai/Girl's Love/GL Manga with binary transgender, non-binary, and intersex characters. Some are headcanons- those are indicated by question marks.
Also, 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?)

Transgender manga without official translations but have (at least partial) fan translations in English. Some of my trans labels are headcanons- those are indicated by question marks.
Organized roughly by release order in Japan.

(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 2: https://myanimelist.net/stacks/55113


Not on MAL (yet):

Natsu no Ane/Summer Sister (2015)
Orie (trans woman) (main)

Chiguhagu/Mismatched (2016)
Tooru/Tohru (trans man) (protagonist)
Yuki (trans woman) (main)

Sakura-chan to Amane-kun/Sakura-chan and Amane-kun (2017)
Sakura (trans girl) (main)
Amane (trane boy) (main)

Hana Ningyou to Danna Sama/The Flower Doll Husband (2019)
Hiromi (trans woman) (protagonist)

Sayonara Chinchin Welcome Manman ~OL ni Naritakute Seibetsu Tekigo Shujutsu shimashita~/Goodbye Chinchin Welcome Manman (I Wanted to Be an Office Lady So I Had SRS) (2019)
Yoriko Kamikawa (trans woman) (protagonist)
*not fully translated

Danshi Jidai no mtf no Manga/Koukousei Hen/MTF Cartoons from the Boys' Era (2019)
Natsuki (trans girl) (protagonist)
*not fully translated

Josei ga Suki na Josei to Otoko datta Josei no Hanashi/The Story of a Girl Who Likes Girls, and a Girl Who Used to be a Guy (2019)
Makoto (trans woman) (main)

Mirai kara kita Jibun ni Onna ni naru you Settaku Sarersu Hanashi/My Future Self Is Persuading Me to Become a Woman (2020)
Yuuka (trans woman) (protagonist)

Otto wa Jitsu wa Josei Deshita/My Husband Who Actually Turned Out to Be My Wife (2020)
Wafuko (trans woman) (main)
*not fully translated

Doumo, Newhalf desu./Hi, I'm Trans (2020)
Tsukasa Andou (trans woman) (protagonist)
Maria (trans woman) (main)
Reiko (trans woman) (main)

Itsuka Shinu Shoujo/A Girl Who Will Die One Day (2020)
Yuuki Akai (trans girl) (main)

Onnanoko ni Naritai Otokonoko no Hanashi/The Story of a Boy Who Wants to Be a Girl (2020)
Girl (trans girl) (protagonist)

Ore no Karada wa Nande Onna Nanda?/Why is my Body Female? (2020)
Ryuutarou Suzumiya (trans man) (protagonist)
*not fully translated

Online Game de Dekita Kareshi ni Real de Aitai to Iwareta Nekama no Otoko no Ko/A G.I.R.L. Whose Boyfriend From an Online Game Wants to Meet Him Offline (2021)
Miyoto (trans girl) (protagonist)

Girlfriend (2021)
Kaoru Shirasaki (trans woman) (main)

Majo ni Naritai Otoko no Ko/The Boy Who Wants to be a Witch (2022)
Koto (trans girl) (protagonist)

Onna no Karada ga Iya nano de Mune o Torimashita/I Hated My Female Body, so I Cut Off My Breasts (2024)
Kazuki (non-binary) (protagonist)

One-shots (one chapter stories) with transgender themes. Some are headcanons- those are indicated by question marks. Also, some are parts of anthologies.
Organized roughly by year.


Not on MAL (yet):

Natsu no Ane (2015)
Orie (trans woman) (protagonist)
*included in Yesterday wo Utatte: afterword

Chiguhagu (2016)
Tooru/Tohru (trans man) (protagonist)
Yuki (trans woman) (main)

Osananajimi Yuri (?) (2017)
College Girl (trans woman) (main)

Josei ga Suki na Josei to Otoko datta Josei no Hanashi (2019)
Makoto (trans woman) (main)

Hana Ningyou to Danna sama (2019)
Hiromi (trans woman) (protagonist)

Murai-kun wa Mizuno-kun wo Dakitai (2019)
Shion Murai (trans boy) (protagonist)
*included in Hagure Idol Jigokuhen

Akarui (2020)
Miki Sanda (trans boy) (protagonist)
*included with Boys Run the Riot

Onnanoko ni Naritai Otokonoko no Hanashi (2020)
Girl (trans girl) (protagonist)

Bokura no VR (2020)
Miharu Akina (trans boy) (main)

Watashi Ki, Oriori to (2020)
Ran Adachi (trans woman) (main)
*included with Last Gender: Nanimono demo Nai Watashitachi

Online Game de Dekita Kareshi ni Real de Aitai to Iwareta Nekama no Otoko no Ko (2021)
Miyoto (trans girl) (protagonist)

Majo ni Naritai Otoko no Ko (2022)
Koto (trans girl) (protagonist)

Doumo, Newhalf desu. (2022)
Tsukasa Andou (trans woman) (protagonist)
Maria (trans woman) (main)
Reiko (trans woman) (main)

Haru to Yakyuu (2023)
Haru (trans girl) (protagonist)

Mukashi no Osanajimi, Otokonoko Janakatta Mitai (2023)
Yuuki (trans woman) (main)


(honorable mentions- trans characters are not the main characters)

Shoujo Bigaku (Kanojo no Yuuwaku) (2006)
Yuno's Brother (trans boy) (supporting)

Unmei no Tori: Takahashi Rumiko Kessakushuu (Unmei no Tori) (2007-2011)
Mai (trans woman) (supporting)

Watashi to Watashi (Watashi to Watashi) (2009-2017)
Miyahara (trans girl) (supporting)

Onnanoko no Sekkeizu (Shounen) (2010-2012)
Miyaji's mom (trans woman) (supporting)

Shindou-ke no Jijou (2014)
Tanaka (trans woman) (supporting)