Could be various causes, get the doctors to check him out. My wife's had headaches since 7 really bad, but not necessarily migraines. We're currently trying to figure out the cause, trying different medications etc.

Could be small seizure activity too, get some diagnostics done. Could be related to something like an AVM, which I had until recently. Birth defect, vein vessel problem, sometimes detected early due to various symptoms. Best to MRI or similar and see if there is anything going on.