Others are right: Hormones can play a part; so can school stresses. If the are truly "little" headaches they likely are not migraines but have him checked.
Work with him to seek out triggers or stressors: Do these come up on days when he has tests? Or when he has certain types of assignments due that he finds stressful most times?
Also, consider that he may be dehydrated. Few of us drink enough water, and tweens and teens are especially bad about remembering to drink -- at least I find my kid and her peers are, and my daughter always gets a headache if she needs even a little more water; and the water takes care of it. Do the headaches tend to fall on, for instance, days they have a particularly active gym class? Or days he has a sport or other activity? Days he stays late at school for a club or other reason? Days AFTER he has stayed up later than usual due to an evening event he does regularly? ....Sit down with him and work up a log of when they seem to happen or what might trigger them. They may be associated with periods of more physical activity or a longer school day when he is not drinking or possibly even not eating enough at the right times.
If he has never had an exam by an optometrist, but only the pediatrician's eye chart exams, be sure to get him a full exam by an optometrist! Everyone should have this done as a baseline even if nothing is "wrong." This may not be vision-related but it could not hurt to get him an exam if he's never had one (and the ones at the pediatrician's office really don't mean a lot, frankly).