Previous studies indicate that transcranial magnetic stimulation (TMS) with biphasic pulses applied approximately over the primary somatosensory cortex (S1) suppresses performance in vibrotactile temporal discrimination tasks; these previous results, however, do not allow separating perceptual influence from memory or decision-making. Moreover, earlier studies using external landmarks for directing biphasic TMS pulses to the cortex do not reveal whether the changes in vibrotactile task performance were due to action on S1 or an adjacent area. In the present study, we determined whether the S1 area representing a cutaneous test site is critical for perceptual processing of tactile temporal discrimination. Electrical test pulses were applied to the thenar skin of the hand and the subjects attempted to discriminate single from twin pulses. During discrimination task, monophasic TMS pulses or sham TMS pulses were directed anatomically accurately to the S1 area representing the thenar using magnetic resonance image-guided navigation. The subject's capacity to temporal discrimination was impaired with a decrease in the delay between the TMS pulse and the cutaneous test pulse from 50 to 0 ms. The result indicates that S1 area representing a cutaneous test site is involved in perceptual processing of tactile temporal discrimination.