The effects of high frequency repetitive transcranial magnetic stimulation on sensory perception and the pain tolerance thresholds were investigated applying both motor cortex stimulation and medial frontal cortex stimulation in normal study participants. Both the sensory perception and pain tolerance thresholds were significantly increased in the motor cortex stimulation, whereas the pain tolerance thresholds, but not the sensory perception was significantly decreased in the medial frontal cortex stimulation. These results suggest the dissociable modulating effects of sensory and pain perception by the high frequency repetitive transcranial magnetic stimulation on the medial pain regulating system, but not the lateral pain regulating system.