The purpose of the present study was to investigate the effect of repetitive transcranial magnetic stimulation (rTMS) in conjunction with task oriented training, on cortical excitability and upper extremity function recovery in stroke patients. This study was conducted with 31 subjects who were diagnosed as a hemiparesis by stroke. Participants in the experimental (16 members) and control groups (15 members) received rTMS and sham rTMS, respectively, during a 10 minutes session, five days per week for four weeks, followed by task oriented training during a 30 minutes session, five days per week for four weeks. Motor cortex excitability was performed by motor evoked potential and upper limb function was evaluated by motor function test. Both groups showed a significant increment in motor function test and amplitude, latency in motor evoked potential compared to pre-intervention (p < 0.05). A significant difference in post-training gains for the motor function test, amplitude in motor evoked potential was observed between the experimental group and the control group (p < 0.05). The findings of the current study demonstrated that incorporating rTMS in task oriented training may be beneficial in improving the effects of stroke on upper extremity function recovery.