Hourou Musuko

Shuuichi Nitori is a 5th grade student who likes to bake and has always been something of a feminine boy. When he transfers to a new school, Shuuichi is mistaken for his 6th grade sister on his first day. Then he ends up sitting next to Yoshino Takatsuki, a tall, boyish girl who everyone calls "Takatsuki-kun." They both have secrets they can't let anyone know...

The series deals with issues such as being transgender, gender identity, and the beginning of puberty.

(Source: Kotonoha, edited)