Objective: To study the modulation of somatosensory evoked potentials (SEP) using transcranial magnetic intermittent theta burst stimulation (iTBS) over human primary motor (M1) and sensory (S1) cortices. Methods: Eleven healthy subjects participated to the study. Median nerve SEP were elicited by electrical stimulation at the right wrist before and after 600-pulse iTBS over M1 or S1 of the left hemispheres at the intensity of 80% active motor threshold. Results: iTBS over S1 facilitated the N20o-N20p, N20p-P25 and P25-N33 amplitudes significantly and the maximal effect appeared 15 minutes after the stimulation. The facilitating effect was observed when the initial phase of the current in the brain was directed antero-medially, whereas the facilitation did not appear when the inverted coil direction was applied. On the other hand, no changes were observed after iTBS over M1. The latencies of the measured onsets and peaks were not affected through the experiments. Conclusions: iTBS over S1 has the facilitating effect to the central somatosensory pathway, and the position and direction of the coil are the determinant factors of the effects. Significance: iTBS can be useful technique to induce synaptic plasticity in human central somatosensory pathway.