Does he go to daycare? Are you in a new house? New daycare?
He may be having a reaction to somethihg in the school or house? Raining can cause all the tree spores/mold spores, etc. to be more prominent in the air and can cause headaches. He could have mild allergies to the spores. If he is in a new house/new school it could be caused from the carpeting (glue fumes, etc.)....
If he continues to complain, act out, etc. you might want to get him tested. We have a great place where we go. Integrative Health Specialists at 93rd and Meridian in Indy. Its a bit of a drive, but they use more natural cures/testing supplies and were able to find my son's issues when the traditional allergist could not.
Not trying to alarm you, but want you to know there are many reasons your son could truly have a headache. Watch his eyes too. Does he have any dark circles? Maybe not super dark but circles none the less will tell you he has some allergy symptoms.