Seemed shounen.
Not sure everything is exactly correct but here goes:

It's a martial arts anime where characters have powers and also a target weakness. The male protagonist ends up becoming strong but he is either cursed or afflicted with the weakness of dealing with girls.
I know it's a stretch but shoot your ideas thanks!

master roshi. dragonball z

tons of stories like that

thus cba to help, sorry

+1

There's a mention of a martial arts school but not sure if junior or high school.

sounds more like yamcha.

Asu No Yoichi
Dragons rioting

there's a dude in full metal panic that's like this. but he's not main character.

New information 2000-2005 Dragons rioting was a strong candidate though (Looks interesting).

Bumps

Bump
So about 2000-2005 martial arts school. Shonen type. Super strong guy who is unable to handle girls.