Objective This study aimed to compute phase synchronization of the alpha band from a multichannel electroencephalogram (EEG) recorded under repetitive flash stimulation from migraine patients without aura. This allowed examination of ongoing EEG activity during visual stimulation in the pain-free phase of migraine. Methods Flash stimuli at frequencies of 3, 6, 9, 12, 15, 18, 21, 24, and 27 Hz were delivered to 15 migraine patients without aura and 15 controls, with the EEG recorded from 18 scalp electrodes, referred to the linked earlobes. The EEG signals were filtered in the alpha (7.5−13 Hz) band. For all stimulus frequencies that we evaluated, the phase synchronization index was based on the Hilbert transformation. Results Phase synchronization separated the patients and controls for the 9, 24 and 27 Hz stimulus frequencies; hyper phase synchronization was observed in patients, whereas healthy subjects were characterized by a reduced phase synchronization. These differences were found in all regions of the scalp. Conclusions During migraine, the brain synchronizes to the idling rhythm of the visual areas under certain photic stimulations; in normal subjects however, brain regions involved in the processing of sensory information demonstrate desynchronized activity. Hypersynchronization of the alpha rhythm may suggest a state of cortical hypoexcitability during the interictal phase of migraine. Significance The employment of non-linear EEG analysis may identify subtle functional changes in the migraine brain.