J.S.
I can't believe I'm typing this...
I had a UTI a few years ago and it felt more like I had been kicked in the testicles.
If it feels like something poking or pricking (trying so hard not to make any puns) - I would think two things - either a bug bite/splinter or the little dude got it caught in the zipper and is still feeling it.
If you don't see any marks on the skin - I'd take him to the doc.
If there are marks on the skin - I'd try to determine when the hurting started to see if it's something innocuous.