Majutsushi Orphen Hagure Tabi
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Manga that involve the use of magic excluding isekai.
Only includes one title from each series as some have a ridiculous amount of titles.

Trans characters from Shounen and Seinen manga. Some are headcanons- those are indicated by question marks. Organized roughly by year.

Manga version part 2: https://myanimelist.net/stacks/64215
Manga version part 3: https://myanimelist.net/stacks/64216
Anime version: https://myanimelist.net/stacks/63974


Not on MAL (yet)

Otomeza no Jun (1982)
Jun (trans woman) (main)

Barcode Fighter (1992)
Sakura Arisugawa (trans girl) (main)

Umanbo! (1995-1996)
Manko Ushida (trans woman) (protagonist)



(bonus shounen/seinen manga- not labelled as shounen/seinen on MAL, but are on other sites, so IDK)

Boku no Futatsu no Tsubasa (2002-2005)
Mako Kashiwagi (intersex girl) (main)
Mako's dad (intersex man) (minor)

Strange Mansion (2004-2006)
Yuuko Shirahai (trans woman?) (main)