My son has been running a fever since yesterday....?!

My son has been running a fever since yesterday....?

He's been saying his head, mouth and stomach hurts...he hasn’t been sick though. I took him to the doctors today and the doctor just prescribed meds for his fever and whatever pains he’s having but still don’t know exactly whats wrong. Hes just lying around running a fever....
every other time he ran a fever, something else was visibly wrong, he had the flu, or a sore throat, etc. I just dont like not knowing exactly whats wrong...the doc didnt help much.

Did this ever happen to you or one of your kids? (hes 3)

First thing I would check would be teeth. Is he getting any new molars? My boys seemed to always do this when they were cutting "big teeth".
My second guess is sinus. That would explain the pain and the temp. Head from the sinus, mouth from pressure and stomach from drainage. Try and ask does the top or bottom of his mouth hurt. Or have him point to where it hurts in his mouth. If it is the top back teeth and no signs of new molars, I would bet sinus. I have three boys and this seems to have been the hardest condition for our doctor to diagnose. They kept telling us it was a bad virus. Hope it helps.