Welcome to e health forum.
Since the CT scan is normal and has not detected any form of increased intracranial pressure, other organic causes of headache have been effectively ruled out.
The probable cause of your 9 year old sons symptoms might be due to migraine.
High levels of stress and anxiety triggered by problems with peers, teachers or parents can play a role in migraine. Children with depression may complain of headaches, particularly if they have trouble recognizing feelings of sadness and loneliness.
You can treat your kid's headache at home with rest, decreased noise, plenty of fluids, balanced meals and over the counter (OTC) pain relievers.
Consultation with a neurologist will help to make a proper diagnosis, so that effective therapy can be initiated.