Asa Made Jugyou Chu!

See Me After Class (朝まで授業chu!, Asa Made Jugyō Chu!) is a Japanese manga series written by Akiyoshi Ohta and illustrated by Munyū. It was adapted into an original video animation in 2012.

Plot
Kagami Yuuki has managed to become a scholarship student in a high-class high school. Unfortunately, thanks to his gender-ambiguous name, the teacher Kakinozaki Ayana has registered him as a girl! It's apparently an uncorrectable mistake, so now Yuuki must live in the girl's dormitory of his new (co-ed) high school.

At least Ayana's willing to take responsibility for her mistake; she volunteers to be his roommate. As one would guess, he and Ayana must make sure none of the other girls in the dorm find out he's actually a boy. Therefore, except for when he's in his classes, Yuuki has to cross-dress, or else both he and his teacher will be kicked out of the school and dorm!

Other Sources

 * Wikipedia
 * Anime News Network
 * MyAnimeList
 * English Digital Manga Volume 1
 * English Digital Manga Volume 2