Dysphagia is a common functional impairment after stroke, resulting in aspiration of liquids, ingested foods, or oral secretions and influencing the quality of life. Noninvasive repetitive transcranial magnetic stimulation has been widely used for rehabilitation of dysphagia. The purpose of this meta-analysis was to investigate the efficacy of repetitive transcranial magnetic stimulation on poststroke swallowing impairment. Four databases were systematically searched for eligible studies from their inception to 31 September 2021. Review Manager 5.4 software was used for this meta-analysis. The bias of included randomized controlled trials was assessed using the version 2 of the Cochrane risk-of-bias tool for randomized trials. Nine randomized controlled trials involving 393 patients were included according to the selection criteria. The results revealed significant benefit of repetitive transcranial magnetic stimulation as a treatment of dysphagia following the onset of stroke, when compared with intervention without repetitive transcranial magnetic stimulation. Applying repetitive transcranial magnetic stimulation on different stimulation sites effectively improved the dysphagia of poststroke patients, and no significant difference was observed among the different stimulation sites subgroups. Our findings support repetitive transcranial magnetic stimulation as an effectively treatment of the poststroke dysphagia, especially in unilateral hemispheric stroke patients.