Blue Wars

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Manga with transgender girls/women.

Part 2: https://myanimelist.net/stacks/29603
Part 3: https://myanimelist.net/stacks/37567
Part 4: https://myanimelist.net/stacks/46068


Not on MAL (yet):

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

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

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

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

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

Umanbo!
Manko Ushida (trans woman) (protagonist)

Otomeza no Jun
Jun (trans woman) (main)

Mirai kara kita Jibun ni Onna ni naru you Settaku Sarersu Hanashi
Yuuka (trans woman) (main)

Danshi Jidai no mtf no Manga/Koukousei Hen
Natsuki (trans girl) (protagonist)

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

Natsu no Ane
Orie (trans woman) (main)

Itsuka Shinu Shoujo
Yuuki Akai (trans girl) (main)

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

Massugu Aoide
Aoi (trans girl) (main)

Oppai wo Totta Kareshi.
Aoi Ishikawa (trans girl) (main)

Barcode Fighter
Sakura Arisugawa (trans girl) (main)

Chiguhagu
Yuki (trans woman) (main)

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

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

Woman with Flowers
Jae-Hee (trans woman) (main)

Girlfriend
Kaoru Shirasaki (trans woman) (main)

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

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

Hana Ningyou to Danna Sama
Hiromi (trans woman) (protagonist)

Yasashii Rival
Marika (trans woman) (main)

Haru to Yakyuu
Haru (trans girl) (protagonist)

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

LGBT (gay, lesbian, bisexual, pansexual, queer, binary transgender, non-binary, genderqueer, intersex, asexual, aromantic, etc.) parents in manga.

Gender-bending (sex changing through supernatural methods) characters who turn out to like their new gender and come out as transgender. Some are debatable.

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)

Transgender manga without official translations but have (at least partial) fan translations in English. 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)