A Meta-analysis was conducted to investigate the effect of repetitive transcranial magnetic stimulation (rTMS) on post-stroke dysphagia (PSD), with different frequencies and stimulation locations, and on the improvement of swallowing-related quality of life. Methods: Multiple electronic databases were searched for randomized controlled trials which met the included standards. Cochrane handbook 5.1.0 and RevMan 5.3 software were separately used for the quality evaluation and Meta-analysis. Results: A total of 17 articles with 629 patients were included. The results had shown that rTMS could more effectively improve PSD than that of the conventional swallowing therapy in convalescent stage (P＜0.05), high-frequency rTMS on bilateral sides or unaffected side and low-frequency rTMS on unaffected side could effectively improve PSD (P＜ 0.05). And rTMS had no significant effect on improving the swallowing-related quality of life in the patients with PSD (P＞0.05). Conclusion: In convalescent stage, high-frequency rTMS on bilateral sides or unaffected side and low-frequency rTMS on unaffected side could effectively improve PSD, but there was no significant improvement in the swallowing-related quality of life in PSD patients.