Found this systematic review on spinal manipulative therapy (SMT) and chronic headaches. Though the authors note that the research isn’t based on strong studies this is their conclusion:
SMT appears to have a better effect than massage for cervicogenic headache. It also appears that SMT has an effect comparable with commonly used first-line prophylactic prescription medications for tension-type headache and migraine headache. This conclusion
rests on a few trials of adequate methodological quality. Before any firm conclusions can be drawn, further testing should be done in rigorously designed, executed, and analyzed trials with followup periods of sufficient length.