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More transgender girls and women in manga. Some are headcanons- those are indicated by question marks.

Part 1: https://myanimelist.net/stacks/28893
Part 3: https://myanimelist.net/stacks/37567
Part 4: https://myanimelist.net/stacks/46068

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. Some are headcanons- those are indicated by question marks.

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)

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)

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):

Atto Iu Man ni Wasureru (Namae no Hanashi)/Things Easily Forgotten (About Names) (2013)
Akane (non-binary) (protagonist)

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

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

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)

Date Aite ga Ikemen ♀ Datta Ken (2023)
Ushio Toudou (non-binary) (main)

Tonari no Trans Shoujo-chan (Taihai Tekina Trans-chan) (2025)
Aikawa (trans girl) (main)

Tonari no Trans Shoujo-chan (Otouto wa Trans-chan) (2025)
Ayumu (trans girl) (main)

Tonari no Trans Shoujo-chan (Mirai kara Kita Trans-chan) (2025)
Yuuka (trans girl) (protagonist)

Tonari no Trans Shoujo-chan (Nitsukawashii Trans-chan) (2025)
Yoshi (trans girl) (main)

Boys Run the Riot: In Transition
Ryou Watari (trans man) (protagonist) (2025)
*sequel to Boys Run the Riot


(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)