Kunoichi Gakuen Ninpouchou - Yogakure

From MangaHelpers:

Ichinose Kouta is transferring to the academy his grandfather runs. He knows little about it, except for the fact that the students are mostly female, so he imagines that his life will soon become a delightful harem-type story.

When he gets lost on the way to the isolated school, he finds out there's a lot his grandfather didn't tell him. The school is actually an all-girls school for ninja! At first, the girls think he's an intruder, and he barely escapes with his life! Luckily, the misunderstanding is cleared up, and he finds himself under the protection of the beautiful and deadly student council president, Fuyunagi Rindou.

But even now, his life will be anything but uneventful, as he finds himself in the middle of an ongoing conflict between Fuyunagi's student council and another student group, headed by a girl known as Momochi Yayoi. [tethysdust]