The evidence regarding efficiency of repetitive transcranial magnetic stimulation (rTMS) on relief of neuropathic pain (NP) in patients with prior spinal cord injury (SCI) is controversial. The current meta-analysis aimed to assess the efficacy of rTMS in pain relieve in patients suffering from SCI associated NP. Medline, PubMed, Cochrane Database, EMBASE, Google Scholar databases were searched for clinical studies on effects of rTMS treatment on NP caused by prior SCI published before March 14th, 2016 with various combinations of following key words: "transcranial magnetic stimulation," "spinal injury," "pain." Standardized difference in means with 95% confidence interval was calculated for the change of pain scores after rTMS or sham rTMS treatments. A total of two randomized controlled studies (RCTs) and 4 crossover RCTs were included in the present meta-analysis. The RCTs recruited a total of 27 patients. The crossover RCTs recruited a total of 100 patients. The combined standardized difference in means indicated that patients who received rTMS intervention had better pain relief than those who received sham rTMS intervention, however, the results did not reach statistical significance (standardized mean difference -0.607, 95% CI: -1.29 to 0.075, P=0.081). rTMS might reduce SCI associated neuropathic pain; however, further studies are required to support our conclusions.