Well, other than pregnancy which is the popular choice.. You could be allergic to something in your bed/room. You could have a mild stomach virus or you're eating food at night that's too acidy. Otherwise, you could be waking up feeling nauseous about another day at school of a stress related issue :)
That use to happen to me when I was younger. I think it's from having touchy stomachs. It use to be if I tried to eat a little to help ease the nausea it would make it worse. Mine started as a kid, I think because my mom would force me to eat an extremely large breakfast and I didn't want it. As I got older eventually the stomach aches disappeared all together. Go get it checked out to be on the safe side.