Background: The clinical efficacy of repetitive transcranial magnetic stimulation (rTMS) protocols on patients with poststroke dysphagia is still unclear. Objective: This trial aimed to explore and analyze the effectiveness of 5 Hz rTMS on the unaffected hemisphere, affected hemisphere, and cerebellum in stroke patients with dysphagia. Methods: This observer-blind and randomized controlled trial included a total of 147 patients with stroke. Patients were divided into four treatment groups: the unaffected hemispheric group, the affected hemispheric group, the cerebellum group and the control group. Each group received traditional dysphagia treatment 5 days a week for 2 weeks. All recruited patients except for those in the control group underwent 10 consecutive rTMS sessions for 2 weeks. For the affected hemispheric group and unaffected hemispheric group, 5 Hz rTMS was applied to the affected mylohyoid cortical region or to the unaffected mylohyoid cortical region. For the cerebellum group, 5 Hz rTMS was applied to the mylohyoid cortical representation of the cerebellum (4.3 cm lateral and 2.4 cm below the inion). The Fiberoptic Endoscopic Dysphagia Severity Scale (FEDSS), Penetration/Aspiration Scale (PAS), Gugging Swallowing Screen (GUSS), and Standardized Swallowing Assessment (SSA) were used to evaluate clinical swallowing function before the intervention (baseline), immediately after the intervention and 2 weeks after the intervention. Results: There were significant time and intervention interaction effects on the FEDSS, PAS, SSA, and GUSS scores (p < 0.05). In a direct comparison of the swallowing parameters of the four groups, the changes in FEDSS, PAS, SSA, and GUSS scores showed a significantly greater improvement in the unaffected hemispheric group, the affected hemispheric group and cerebellum group than in the control group (p < 0.05). Conclusions: Whether stimulating the unaffected hemisphere or the affected hemisphere, 5 Hz high-frequency rTMS on mylohyoid cortical tissue might have a positive effect on poststroke patients with dysphagia. In addition, cerebellar rTMS is a safe method that represents a potential treatment for poststroke dysphagia, and more clinical trials are needed to develop this technique further. Clinical Trial Registration: chictr.org.cn, identifier: ChiCTR2000032255.

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