I frequently wake up with a headache. These are diagnosed migraines. The pattern is recognized, as the timing of migraines is a stress-recovery phenomenon- the headache generally occurs as the body is recovering from exertion. Which is pretty insidious, since it's hard to know that you're triggering a migraine until it's too late.

I don't know if your headaches are migraines. If they are, there are prophylactic approaches to preventing them, which may or may not work for you (they didn't for me). Best of luck.