Mei no Naisho revolves around the life of the title character Mei Haruna, an effeminate young boy who was raised by his witch mother as a girl, and always thought of himself as female. His mother was the only family he had, so after she died, he transfers to an all-girls high school and resides in the school's dormitory with his familiar Abel, who is talking cat, and his roommate Fuuka Honjou, who is a member of the public morals committee.

Shortly after arriving at the school, his new friends discover after a magical display in the dormitory community bath that he is actually male, though this comes as quite a shock to him despite him being aware of the physical differences between him and normal girls. Despite him being found out, and after some helpful intervening of the perverted student council president, the principal of the school decides that he can stay at the school.

The next day, Mei comes to school with Fuuka and apologizes for hiding the fact that he was a witch, and informs the others how he is apparently male. The other students quickly accept him as one of their own, and are impressed how he can use magic.

From MangaHelpers:
Before they enter high school, the boys Meguru and Shou are whining about the fact that neither of them has a girlfriend. A strange, large-breasted woman shows up, claiming that she will fix their problem, and kisses Meguru. This odd occurrence is pushed out of the boys' minds when they meet up with Souko, a friend from elementary school, who is going to be in their high school. She's grown up into a pretty young girl, and it seems like the boys might have a shot with her!
That evening, Meguru realizes that the strange kiss may have had more meaning than he thought: he's turned into a girl! He convinces Shou and his mother of his identity, but no one has any idea how to turn him back. Now he's going to have to learn how to be a girl and let go of his hope of dating his cute childhood friend Souko. What will happen to his hopes for a popular high-school life?