Negapoji ~Onii-chan to Yobanaide!!~

Hiroba Mahiru, the protagonist, is a girl attending Mizuki Academy. One day in the changing rooms at school, Mahiru's friend Kasumi Sakuraba accidentally tore off her panties. After what she saw, Kasumi declared Mahiru was a boy. After this, Mahiru was forced to go to the hospital for two months, before finally being able to return to school...

...but as a boy instead.

[Translated from Japanese Wikipedia]