BACKGROUND Supernumerary phantom limb (SPL) caused by spinal cord injury (SCI) has previously been reported in several studies. However, the mechanisms and management of SPL in SCI patients are still not fully understood. Herein, we report a rare case of SPL in a patient with incomplete SCI. CASE SUMMARY A 46-year-old man complained of four hands 7 d after SCI. He was diagnosed with SPL complicated with actual limb neuropathic pain. Following a period of treatment with neurotrophic agents and Chinese traditional and analgesic medications, SPL symptoms and actual limb pain did not improve. However, his symptoms gradually lessened after combined treatment with high-frequency repetitive transcranial magnetic stimulation (rTMS), a promising neuromodulation technique, over the M1 cortex and visual feedback. After 7 wk of this treatment, SPL disappeared completely and actual limb pain was significantly relieved. CONCLUSION Cerebral plasticity changes may be a mechanism underlying the occurrence of non-painful SPL in SCI patients, and high-frequency rTMS applied to the M1 cortex could be a promising treatment method for SPL.