Yes, I have experienced this, as well as one of my children.
If he is on antihistamine (even if he isn't), it could be dry air and not enough blinking or tear production. The simple solution the doctor gave for my daughter was a liquid tears type eye drops.
Another problem can be allergy reactions themselves, and not necessarily in both eyes. This can happen from contact from his own hand.
And then of course... the glasses.... my daughter did not complain her eyes hurt when she needed glasses - just that she couldn't see well. BUT - some kids start rubbing eyes and saying their eyes hurt because of straining to see, and possibly not blinking.