Repetitive transcranial magnetic stimulation (rT) could change the excitability of the cerebral cortex, and control the neurotransmitter release, with the therapeutic effect depending on stimulation intensity and position. In this study, we used 3 Hz rTMS to stimulate the pharyngeal cortical area of the lesioned hemisphere and to explore its clinical significance in the treatment of dysphagia after acute cerebral infarction.A total of 61 in-patients with acute dysphagia caused by cerebral infarction hospitalized in the department of neurology of our hospital were included in this study and were assigned into the control and rTMS group. Patients in the control group only accepted the basic treatment of rehabilitation training, while patients in the rTMS group received additional rTMS (3 Hz) stimulation. The levels of the water swallowing test (WST) 14 days before and after the treatment of rTMS (3 Hz) would be recorded.After different therapies in two groups, 9 patients of the control group showed excellent curative effect, with a recovery rate of 31.0%. However, in the rTMS group, the swallowing function of 21 patients was significantly improved, with a recovery rate of 65.6%. Comparison results showed that the recovery rate of the rTMS group was much better than the control group (P < 0.05), indicating an effective therapeutic effect of 3 Hz rTMS on patients with dysphagia after acute cerebral infarction.Stimulating the target cortical representation areas of pharyngeal of the lesioned hemisphere with cerebral infarction by the rTMS (3 Hz) could improve the patients' function.© 2021. Fondazione Società Italiana di Neurologia.