Not exactly like the title says, but more like a boy for some reason is able to do things that are normally considered a girls only kind of things. By things I mean supernatural things. Like the ones where Mc awakens powers that are said to be awoken by girls. I don't know how to explain it... JP, Romance, and no harem ending if possible please~
I can only think of 2 anime’s off the top of my head, not sure they have novels or not. Alright so i just checked and they both have novel versions, tho I don’t know anything about them since I haven’t read them. Anyway, 1) Unlimited Fafnir, this one basically fits all your descriptions but I don’t know about them ending and whether or not it’s a harem ending, srry. 2) Infinite Stratos, The more I thought about it this doesn’t rlly fit your taste but decided to put because I said I thought of 2. This one isn’t supernatural power but mecha suits, also this one is kinda hard harem but not sure Mc picks a girl at the end, again srry I couldn’t be of much help.
How can you have a boy in an all girls school and not have a harem? That's literally the point of such a set up.
AHHHHHH I JUST THOUGHT OF ANOTHER ONE. 3) Trinity Seven, not sure if its an all girls school but I basically can't remember seeing another boy in the anime besides the principal. Also this is a harem but I can't remember if ending is harem or not srry. But its also one of my favorite amines so I recommend giving it a look.