To systematically evaluate the impact of repeated transcranial magnetic stimulation (rTMS) on the rehabilitation outcomes of patients with spinal cord injury (SCI). Methods: Computerized searches were conducted in electronic databases including PubMed, Web of Science, Embase, Cochrane Library, CNKI, Wanfang, VIP, and China Biology Medicine for randomized controlled trials (RCTs) on rTMS treatment for SCI. The search period covered from the inception of each database to September 21, 2023. Outcome indicators included the Spinal Cord Independence Measure (SCIM), Functional Independence Measure (FIM), Barthel Index (BI), Resting Motor Threshold (RMT), Motor Evoked Potential (MEP) amplitude, Lower Extremity Motor Score (LEMS), Walking Index for Spinal Cord Injury II (WISCI-II), Modified Ashworth Scale (MAS), and Visual Analog Scale (VAS) for pain. Risk of bias was assessed using tools recommended by the Cochrane Handbook for Systematic Reviews of Interventions, and Meta-analysis was performed using RevMan 5.4 software. Results: A total of 23 RCTs involving 1 478 patients were enrolled. Meta-analysis results showed significant improvements in the rTMS treatment group compared to the control group in SCIM score [MD=6.93, 95% CI (5.48, 8.37), P< 0.00001], FIM [MD=16.17, 95%CI (11.66, 20.69), P<0.00001], BI score [MD=10.43, 95%CI (5.17, 15.69), P< 0.00001], RMT [MD=－3.99, 95%CI (－4.88, －3.09), P<0.00001], MEP amplitude [MD=0.33, 95%CI (0.23, 0.43), P<0.00001], LEMS [MD=5.47, 95%CI (3.80, 7.14), P<0.00001], WISCI-II [MD=1.79, 95%CI (1.41, 2.18), P<0.00001], MAS score [MD=－0.15, 95%CI (－0.20, －0.10), P<0.00001], and VAS pain score [MD=－1.37, 95%CI (－1.66, －1.08), P<0.00001]. Conclusion: rTMS treatment is beneficial for SCI patients in improving functional independence and activities of daily living, ameliorating lower extremity motor dysfunction, and alleviating neuropathic pain and spasms.