Background: Previous studies have demonstrated the effectiveness of repetitive transcranial magnetic stimulation (rTMS) in treating post-stroke dysphagia (PSD). However, consensus on optimal clinical protocols for rTMS remains unclear. This study systematically evaluated the efficacy and safety of rTMS with different stimulation parameters in the treatment of PSD to provide evidence-based recommendations for clinical practice.Methods: Following Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines, related randomized controlled trials (RCTs) were searched across five databases (PubMed, Web of Science, Embase, Cochrane Library, MEDLINE) up to November 2024. Two reviewers independently screened studies, extracted data, and assessed quality using RevMan 5.40. Heterogeneity was evaluated via I² values, with fixed/random effects models applied accordingly.Results: A total of 18 RCTs with 835 PSD patients were included in this study. The overall risk of bias in the included trials was evaluated as low, and the level of evidence recommendation was rated as “strong.” Meta-analyses demonstrated that both cerebral and cerebellar rTMS treatments significantly improved the swallowing function of PSD patients (p < 0.05). Subgroup analysis of cerebral rTMS showed that high-frequency rTMS (HF-rTMS) could effectively improve the swallowing function of PSD patients (p < 0.05), while low-frequency rTMS (LF-rTMS) failed to improve the swallowing function of PSD patients compared with the control group (p > 0.05). Furthermore, bilateral cerebral rTMS demonstrated superior efficacy in enhancing swallowing function compared to unilateral cerebral rTMS (p < 0.05). Subgroup analyses based on the Penetration Aspiration Scale (PAS) and Dysphagia Outcome Severity Scale (DOSS) revealed that cerebellar rTMS was more effective than cerebral rTMS in improving swallowing function in patients with PSD (p < 0.05). Regarding safety profiles, only 5 of the 18 RCTs documented mild and transient adverse events, including isolated cases of dizziness, headache, and temporary hearing impairment during treatment sessions.Conclusion: Both cerebral and cerebellar rTMS therapy can effectively and safely improve swallowing function in patients with PSD. Furthermore, cerebellar rTMS appears to be superior to cerebral rTMS in the treatment of PSD.Systematic review registration: https://www.crd.york.ac.uk/PROSPERO/view/CRD42024498567.