My migraine always come from an internal conflict, usually one that involves my intuition.
I have not found them to be related to the work I do as a professional intuitive. Meaning that even though I am constantly using my abilities with clients, that does not give me a migraine.
But they come up when I have a personal conflict where I *know* something intuitively about my life but I'm resisting it. For example: I used to be scared of my own intuitive skills. I didn't want to know all these things about other people, so the migraines would come. The pain would mask thing I didn't want to see/feel.
What works for me is to either getting a reading from a friend who is also intuitive to help pinpoint the conflict or figure it out on my own, usually by asking my spirit guide.