I have been doing yoga but I notice that when I do the Energization Exercises, especially the ones in which we have to look up, or bend sideways or downward, in the set of yogic exercises, my crown chakra begins to have a lot of pain. It may be an indication of migraine. But the point is that it hinders my exercises since the pain lasts sometimes for days. As such I am reluctant to do those exercises which involve too much of head movement or looking up. My meditation is fine, about half hour only though.
I would strongly recommend that you consult a physician to find out if there is a physical reason for the pain in your head.
Usually there should be no problem with any of the head movements involved in the Energization Exercises or in the yoga asanas. For now, avoid any of the exercises that cause you pain and simply do them mentally rather than physically.