This study sought to systematically evaluate the prophylactic and therapeutic effects of low-intensity transcranial ultrasound stimulation on migraine in rats. We used video recordings to assess the head scratching behavior and laser speckle contrast imaging to record the changes in cerebral blood flow velocity of freely moving rats in a healthy group, migraine group, migraine group with ultrasound prevention, and migraine group with ultrasound therapy. Results demonstrated that (1) head scratching during migraine attacks in rats was accompanied by an increase in cerebral blood flow; (2) both ultrasound prevention and therapy significantly reduced the number of head scratches but did not reduce the cerebral blood flow velocity; and (3) the number of head scratches in the ultrasound stimulation groups was not affected by the auditory effect. These results reveal that low-intensity ultrasound has the potential to be used clinically in the prevention and therapeutic treatment of migraine.