The aim of this study was to investigate whether repetitive transcranial magnetic stimulation (rTMS) can improve motor recovery in the lower extremities of the patients with subacute stage spinal cord injury (SCI). This study was conducted with 19 subjects diagnosed with paraplegia because of SCI. The experimental group included 10 subjects who underwent active rTMS, and the control group included 9 subjects who underwent sham rTMS. The SCI patients in the experimental group underwent conventional rehabilitation therapy, and active rTMS was applied daily to the hotspot of the lesional hemisphere. The SCI patients in the control group underwent sham rTMS and conventional rehabilitation therapy. The participants in both the groups received therapy five days per week for six weeks. Latency, amplitude, and velocity were assessed before and after the six-week therapy period. A significant difference in post-treatment gains for the latency and velocity was observed between the experimental and control groups (p < 0.05). However, no significant differences in the amplitude were observed between the two groups (p > 0.05). The results of this study indicate that rTMS may be beneficial in improving motor recovery in the lower extremities of subacute stage SCI patients.