The aim of this study was to evaluate the effect of repetitive peripheral magnetic stimulation at two different frequencies (20 and 30 Hz) on cortical excitability in motor areas related to swallowing in healthy individuals. The study participants were 10 healthy normal volunteers (two women and eight men, age range 25–36 years). Repetitive peripheral magnetic stimulation was applied to the submandibular muscle using a parabolic coil at the site where contraction of the suprahyoid muscles was elicited. Stimulation was continued for 10 min (total 1200 pulses) at 20 Hz on 1 day and at 30 Hz on another day, with the stimulation strength set at 90% of the intensity that elicited pain. The motor-evoked potential amplitude of suprahyoid muscles was assessed before, immediately after, and 30 min after stimulation. Stimulations at both 20 and 30 Hz significantly increased motor-evoked potential amplitude (P<0.05), with the increase maintained until 30 min after stimulation. The motor-evoked potential amplitude immediately after stimulation was not significantly different between the 20 and 30 Hz frequencies. The results indicated that repetitive magnetic stimulation increased motor-evoked potential amplitude of swallowing muscles, suggesting facilitation of the motor cortex related to swallowing in healthy individuals.