Like headaches, your child's upset stomach is probably caused by something other than stress. It may be from eating too much or eating something that disagreed with him. A minor illness, needing to go to the bathroom, or not feeling well may be the cause. If the discomfort is not severe or continuing, rest, a little sympathy, and some personal space are usually right on target.
An upset stomach is more likely to be caused by stress than are headaches. When the sign is caused by stress, your child is feeling edgy and afraid of something or someone. Sensitivity on your part is important. Gently encouraging him to talk about what is wrong usually helps a lot.
If talking is not easy for him, this is a good approach. "I'll bet your stomach is telling you you are afraid or a little uptight about something or someone. Does it have something to do with things here at home, or at school, or maybe with your friends?" If this gets a response, listen, being careful not to pass judgement. Not criticizing your child and not inadvertently implying his feelings are wrong or unimportant are the keys to supportive listening.