ladybusiness | (Reply)

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I'm not sure if it ages well but one of my formative YA reads was Tamora Pierce's Song of the Lioness series, in which the main character trades place with her twin brother to become a squire and later on opens the path for women to be allowed to become knights.

Persona 4 also has a girl who cross-dresses as a boy so people take her more seriously as an investigator and becomes the school heartthrob. I headcanon that character as trans, but this is not explicitly supported by canon. ^^;

And of course, as mentioned above, Hana Kimi (and Ouran High School Host Club) and Monstrous Regiment! And while it's quite not the same I think you might be interested in the anime Kino's Journey which is a gen piece of canon with self-contained episodes and has cross-dressing elements and a lot of Gender in it, if you don't mind something quieter but still very thoughtful. The main character is androgynous and doesn't identify with any gender but they're dressing up like a specific person.