I sometimes get the same really bad headaches, my problem is low blood sugar or hypoglycemia as puppypaws mentioned above. Your doctor can check for this but you probably have to fast for 12 hours before they can do the test. Do you find you get similar headaches if you skip a meal, like lunch for example? I recently switched from Gatoraid (half water) to Powerbar endurance and found that I was getting headaches during my ride. I added just a little lemonade mix, 1/3 of the power bar scoop per 24 oz. and it fixed my problem.
But getting it checked out by the doctor is the safest thing.