Objective To systematically analyze the clinical efficacy and safety of repetitive transcranial magnetic stimulation in the treatment of central neurogenic dysphagia. Methods Randomized controlled trials on the treatment of dysphagia by repetitive transcranial magnetic stimulation in domestic and foreign databases were thoroughly searched. The retrieval time ranged from database inception to January 15, 2022. According to the inclusion and exclusion criteria, data were extracted from eligible literatures and analyzed. Literature quality was assessed. Finally, 17 articles (11 English language-published articles and 6 Chinese language-published articles) were included with a total of 857 patients. The Cochrane Collaboration tool and the Physiotherapy Evidence Database were used to evaluate the risk of bias. RevMan software and R language programming were used for statistical analysis. This systematic review was registered on International Prospective Register of Systematic Reviews (PROSPERO; CRD42022304209). Results The results of meta-analysis showed that repetitive transcranial magnetic stimulation significantly reduced the severity of dysphagia (SMD=-0.83, 95%CI: -1.03, -0.63, Z=8.14, P<0.01), improved the Standardized Swallowing Assessment (SSA) score (MD=-3.14, 95%CI: -3.70, -2.57, Z=10.84, P<0.01), the Water Swallow Test (WST) score (MD=0.95, 95%CI: 0.82, 1.07, Z=15.05, P<0.01), the Penetration-Aspiration Scale (PAS) score (MD=-0.41, 95%CI: -0.63, -0.19, Z=3.68, P<0.01), surface electromyography (sEMG) parameters (SMD=-0.47, 95%CI: -0.77, -0.16, Z=2.99, P<0.01) and the Barthel Index (BI) (MD=22.50, 95%CI: 13.67, 31.32, Z=4.99, P<0.01). There were no significant differences in the pharyngeal transit time (PTT) (MD=-0.07, 95%CI: -0.16, 0.02, Z=1.45, P=0.15) and the incidence of adverse events (RR=2.63, 95%CI: 0.85, 8.14, Z=1.68, P=0.09). Conclusion Repetitive transcranial magnetic stimulation has a certain clinical effect in the treatment of central neurogenic dysphagia, which can reduce the severity of dysphagia, improve swallowing safety, efficiency, and daily living ability, without obvious adverse events. However, it does not significantly improve the PTT. More high-quality studies are still needed to verify the above conclusions.