Hourou Musuko

 放浪息子 / Wandering son

The story center on a 5th grade biy named Shuuichi Nitori who is mistaken for his 6th-grade sister as he looks very feminine. He happens to sit next to Takatsuki Yoshino, a girl who wishes she was a boy. Both of them have secrets they cannot tell anyone. 

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