Repetitive transcranial magnetic stimulation (rTMS) has been known to improve the motor function through modulation of excitability in the cerebral cortex. However, most studies with rTMS were limited to post-stroke patients with mild to moderate motor impairments. The effect of rTMS on severe upper-limb motor impairment remains unclear. Therefore, this study investigated the effects of rTMS on the upper extremity function in post-stroke patients with severe upper-limb motor impairment. Subjects were divided into 3 groups, low-, high-frequency rTMS and control group were received stimulation 10 times for 2 weeks. The motor scale of Fugl-Meyer Assessment (FMA) and cortical excitability on the unaffected hemisphere were measured before and after performing 10 rTMS sessions. The motor scale of upper extremity FMA (UE-FMA) and shoulder component of the UE-FMA were significantly improved in both low- and high-frequency rTMS groups. However, no significant improvement was observed in the wrist and hand components. No significant differences were noted in low- and high-frequency rTMS groups. The amplitude of motor evoked potential on the unaffected hemisphere showed a significant decrease in the low- and high-frequency stimulation groups. rTMS may be helpful in improving upper extremity motor function even in post-stroke patients with severe upper-limb motor impairment.