It sort of fits? The mc doesn't actually become a girl, but he disguises himself as one by crossdressing in order to get inside his younger sister's school and help her out. It's a really funny read, and I def recommend!
Not exactly the same, but natsume's book of friends is similar in that a kid has a mysterious family history and can see otherworldly beings. But it has a gentler feel and more episodic storyline.
Is this based on a novel? And if it is, is there any link where I can read it? Thank you!