Phonophobia is a cardinal symptom in migraine, and migraineur may have impaired habituation of brainstem auditory evoked potential (BAEP). High-rate repetitive transcranial magnetic stimulation (rTMS) has been found effective in migraine, but its effect on brainstem excitability has not been evaluated. We report the effect of high-rate rTMS on ictal phonophobia, hearing threshold (HT), and BAEP as the biomarkers of impaired habituation in the patients with migraine. Forty-three migraineurs and 31 healthy controls were included. Their headache frequency and severity were noted, and ictal phonophobia was recorded on a 0-4 scale at baseline and one month after rTMS. Hearing threshold and three consecutive BAEP at 40 dBSL, 50 dBSL, and 60 dBSL were recorded at baseline and repeated after the 3rd session of rTMS. Peak latencies and amplitudes of BAEP waveforms were measured. Three sessions of 10 trains of 10 Hz rTMS were delivered over the left motor cortex corresponding to the hot spot of the abductor digiti minimi. Consecutive 3 tracings of BAEP at 40 dBSL, 50 dBSL, and 60 dBSL revealed increasing amplitudes of wave III and IV in migraineurs, which persisted even after rTMS. At 60 dBSL, wave III amplitude was higher in migraineurs compared to the control, and remained so after rTMS. The severity of phonophobia and HT, however, improved after rTMS. Migraineurs had improvement in phonophobia and HT following rTMS, which did not commensurate with the biomarkers of impaired habituation in BAEP. However, longer trains and multiple sessions of rTMS may be explored in further study.