Shuuichi Nitori is a fifth-grade student who enjoys baking and has always been somewhat feminine. Upon transferring to a new school, he is mistaken for his sixth-grade sister on his first day. He then ends up sitting next to Yoshino Takatsuki, a tall, boyish girl whom everyone calls "Takatsuki-kun." Both of them harbor secrets they cannot reveal to anyone... The series addresses topics such as being transgender, gender identity, and the onset of puberty.