Onani Master Kurosawa(2007)

Kakeru Kurosawa is an asocial junior high school student. He rarely associates with his classmates, and he looks down on them. But this behavior is topped off by a certain bad habit, his closely guarded secret: every day after school, he sneaks in to the rarely used girls' toilet on the 3rd floor and masturbates in a stall. Kakeru's shadowy routine remains undisturbed until one day, when a diminutive girl from his class, Aya Kitahara, almost discovers him. Their meeting begins a coming-of-age story dealing with blackmail, bullying, revenge, heartbreak, and ultimately, redemption.

(Source: Anime News Network)

Note: Includes one extra chapter.