Dysphagia caused by brain stem injury is the most difficult type to recover among all types of swallowing disorders. Repetitive transcranial magnetic stimulation (rTMS) is a safe and effective treatment for swallowing disorders, but there is no unified standard or complete treatment plan for the use of rTMS parameters (frequency, intensity, time) and specific action sites in the treatment of cyclopharyngeal muscle retardation caused by brainstem injury after stroke. This article reviews the research literature on rTMS treatment of post-stroke cyclopharyngeal muscle retardation in recent years in order to conduct further research and find a systematic treatment plan.