Purpose: We tested whether repetitive transcranial magnetic stimulation (rTMS) improved recovery following spinal cord injury (SCI) in rats with transplantation of adipose tissue-derived stromal cells (ATSCs). Methods: Twenty Sprague-Dawley rats (200-250 g, female) were used. Moderate spinal cord injury was induced at the T9 level by a New York University (NYU) impactor. The rat ATSCs (approximately $5{ imes}10^5$ cells) were injected into the perilesional area at 9 days after SCI. Starting four days after transplantation, rTMS (25 Hz, 0.1 Tesla, pulse width=$370{mu}s$, on/off time=3 sec/3 sec) was applied daily for 7 weeks. Functional recovery was assessed using the Basso, Beattie, and Bresnahan (BBB) locomotor rating scale as well as pain responses for thermal and cold stimuli. Results: Both groups showed similar, gradual improvement of locomotor function. rTMS stimulation decreased thermal and cold hyperalgesia after 7 weeks, but sham stimulation did not. Conclusion: rTMS after transplantation of ATSCs in an SCI model may reduce thermal hyperalgesia and cold allodynia, and may be an adjuvant therapeutic tool for pain control after stem cell therapy in SCI.