Fujioka Haruhi wins a scholarship to attend Ouran Academy, a school reserved for only the most rich and prestigious. Despite what other students may think of her, she cares little for physical appearances or the fact that she is a commoner.

The story is set in Heavenly Host Elementary School, an elementary school that was torn down following the murders and disappearances of several of its staff and students. By the start of the story, another school called Kisaragi Academy has been built over the elementary school site.