Objective To observe the clinical effect of repetitive transcranial magnetic stimulation (rTMS) combined with balloon dilatation and routine swallowing training on dysphagia caused by cricopharyngeal dysfunction (CPD) after stroke. Methods Patients with dysphagia after stroke who were hospitalized at Hubei Provincial Hospital of Integrated Chinese and Western Medicine between January 2022 and February 2023 were selected. The patients were divided into the trial group and the control group by random number table method. The control group received balloon dilatation and routine swallowing training, and the trial group received rTMS based on the treatment plan of the control group. All patients were treated for 3 weeks. The videofluoroscopic swallowing study (VFSS), Penetration Aspiration Scale (PAS), and Functional Oral Intake Scale (FOIS) were used at pre-therapy and 3 weeks after treatment to assess the improvement of swallowing function. Results A total of 49 patients were included, including 25 in the trial group and 24 in the control group. There was no statistically significant difference in age, gender, course of disease, stroke type, and swallowing function before treatment between the two groups of patients (P>0.05). After 3 weeks of treatment, the VFSS dysphagia scores (Z=−4.465, −4.327, P<0.001) of the trial group and the control group were higher than those before treatment, and the trial group was better than that in the control group (t=2.099, P=0.041). The PAS scores (Z=−4.179, −3.729, P<0.001) and FOIS scores (Z=−4.476, −4.419, P<0.001) of the trial and control groups were improved after treatment, and the improvement of the PAS score (t=−2.088, P=0.042) and FOIS score (Z=−2.134, P=0.033) in the trial group were more significant (P<0.05). No serious adverse reactions were observed in patients during the study process. Conclusion The rTMS combined with balloon dilatation and routine swallowing training can significantly improve the swallowing function of patients with dysphagia caused by CPD after stroke, and further improve its clinical efficacy, worthy of clinical application.