I would ask for 2nd opiinion on MRI and CT scan to be sure..Is he seeing a pediatric Neurologist? Where ever you live-go online and look for specialist in your area..Call your sons PCP and ask him/her to recommend someone..Tell them you are worried..
I know I might sound like a broken record but-not syaing your son has this--
My sister was having so called migraines for years-whena MRI was finally done it showed a huge mass that was diagnosed as a Menangioma..
You said yor son is an athelete-has he been hit in the head, could he have a pinched nerve..I'm sure the docs have asked these things..He is 13 could he have taken a drugs without your knowdledge.What caused the headache-how did it begin, is it sharpe, dull,burning..best of luck honey-I hope you get answers soon and help for your son to feel better..