Gonadotropic hormones play an important role in the regulation of emotion. Previous studies have demonstrated that estrogen can modulate appetitive (approach/positive) and aversive (avoidance/negative) affective behaviors during the menstrual cycle. Frontal alpha asymmetry (a measure of relative difference of the alpha power between the two anterior hemispheres) has been associated with the trait and state reactivity of different affective styles. We studied the pattern change of frontal alpha asymmetry across the menstrual cycle. 16 healthy women participated in this resting magneto-encephalographic (MEG) study during the peri-ovulatory (OV) and menstrual (MC) phases. Our results showed significant interaction of resting MEG alpha activity between hemispheric side and menstrual phases. Difference in spontaneous frontal alpha asymmetry pattern across the menstrual cycle was also noted. Relatively higher right frontal activity was found during the OV phase; relatively higher left frontal activity was noted during the MC phase. The alteration of frontal alpha asymmetry might serve a sub-clinical correlate for hormonal modulation effect on dynamic brain organization for the predisposition and conceptualization of different affective styles across the menstrual cycle.