Background. Neuropathic pain often follows spinal cord injury (SCI). Objective. To compare the effect of repetitive transcranial magnetic stimulation (rTMS) applied over different motor cortex targets (hand vs leg area) versus sham stimulation on neuropathic pain and local neurophysiological changes in patients with SCI. Methods. A total of 16 patients with complete or incomplete motor SCI and chronic neuropathic pain participated in a double-blind, cross-over randomized study. Three single sessions of sham or active rTMS (10 Hz, total of 2000 stimuli) were applied in random order over the hand or leg area with a minimal 2-week interval. The main outcome measures were the numeric rating scale for pain sensation and parameters derived from motor mapping of the first dorsal interosseous muscle, including maximal amplitude of evoked response as well as map area, volume, and location. Results. rTMS applied to either the hand or the leg area, but not sham stimulation, induced a significant but equivalent reduction in pain for the first 48 hours postintervention (P < .05). Participants with an incomplete lesion showed greater analgesia than those with a complete lesion (21% vs 3%, respectively; P < .05). The main change observed for motor map measurements was an increase in corticospinal excitability after stimulation of the hand area (P = .04) but not for the other conditions. Conclusion. rTMS applied over the hand or leg motor cortex decreased neuropathic pain regardless of any change in cortical excitability, suggesting that the analgesic effect is not associated with local changes at the motor cortex level itself.