To evaluate brainstem excitability in menstrual migraine (MM) patients and compare the electrophysiological parameters of the trigeminocervical reflex (TCR) during the perimenstrual (headache period) and follicular (headache-free) periods with those in healthy controls. Thirty-one patients with MM and 22 volunteer age- and sex-matched healthy women were included in the study. The TCR was studied bilaterally with stimulation of the supraorbital branch of the trigeminal nerve during the perimenstrual period and follicular phase. The electrophysiological parameters of the TCR were compared between MM patients and controls. In controls, there was no statistically significant difference in the mean reflex latencies recorded during the perimenstrual and follicular phases (P > 0.05). In MM patients, the mean reflex latencies recorded during the perimenstrual (headache period) and follicular phase (headache-free) periods were significantly different from each other and from those in controls. The latencies of MM patients during the follicular (headache-free) period were significantly longer than those of controls. Brainstem excitability differed significantly between the perimenstrual (headache period) and follicular phase (headache-free) periods in MM. Furthermore, trigeminal excitability in MM patients was significantly different from that in healthy controls in both phases of the menstrual period.