Background: Neuromodulation therapy has been used to an adjunctive treatment promoting motor recovery in stroke patients. The objective of the study was to determine the effect of repetitive transcranial magnetic stimulation (rTMS) on neurobehavioral recovery and evoked potentials in rats with middle cerebral artery occlusion. Methods: Seventy Sprague-Daley rats were induced permanent middle cerebral artery occlusion (MCAO) stroke model and successful stroke rats (n=56) assigned to the rTMS (n=28) and sham (n=28) group. The 10 Hz, high frequency rTMS gave on ipsilesional forepaw motor cortex during 2 weeks in rTMS group. The somatosensory evoked potential (SSEP) and motor evoked potential (MEP) were used to evaluate the electrophysiological changes. Behavioral function of the stroke rat was evaluated by the Rota rod and Garcia test. Results: Forty rats ($N_{rTMS}=20;;N_{sham}=20$) completed all experimental course. The rTMS group showed better performance than sham group in Rota rod test and Garcia test at day 11 (p<0.05) but not day 18 (p>0.05). The amplitude of MEP and SSEP in rTMS group was larger than sham group at day 18 (p<0.05). Conclusions: These data confirm that the high frequency rTMS on ipsilesional cerebral motor cortex can help the early recovery of motor performance in permanent middle cerebral artery stroke model and it may simultaneously associate with changes in neurophysiological activity in brain.