There are no studies attempted to determine the effects of different phases of menstrual cycle on frequency following response (FFR) for speech stimuli. The aim of the study was to determine the differences in latencies and amplitude of FFR waves recorded at four phases of menstrual cycle. In addition, it was also attempted to determine if there is any ear effect on latency and amplitude measures across the phases of menstrual cycle. FFR was recorded in 20 females in the age range of 18–25 years in the four menstrual cycles [Phase I—menses (day 1–3), Phase II—proliferative phase (day 11–14), Phase III—mid-luteal phase (day 17–22) and Phase IV—pre-menstrual phase (day 25–27)]. The results of the study showed that there was significant reduction in latencies and slight increase in amplitude during menses and mid-luteal phase compared to mid-cycle and pre-menstruation cycles. The present study supports the hypothesis that difference in the levels of sex hormones in women during menstrual cycle can affect brainstem encoding of speech stimuli.