Background <p>Dysphagia is a frequent and challenging complication after stroke, severely impacting both recovery and quality of life. Conventional rehabilitation approaches often yield limited results, underscoring the need for novel treatments. This work compared the effectiveness of two different repetitive transcranial magnetic stimulation (rTMS) approaches in enhancing swallowing function in post-stroke dysphagia (PSD).</p> Methods <p>This prospective, randomized, controlled trial was conducted with 60 patients, 18–80 years old, diagnosed with acute ischemic stroke and suffered from PSD. Participants were randomized equally to three groups: Group 1 received bilateral facilitatory rTMS targeting both hemispheres, Group 2 received unilateral facilitatory rTMS on the contralesional hemisphere, and Group 3 received sham rTMS.</p> Results <p>Motor threshold (MT) scores were similar across the three groups at baseline (date 0). At follow-up, Group 1 showed significantly lower MT scores than Group 3 at dates 1 and 3 (<i>P</i> &lt; 0.05), with no significant difference between Group 2 and Groups 1 and 3. At date 2, Group 1 had significantly lower MT scores than both Groups 2 and 3 (<i>P</i> &lt; 0.05), while scores between Group 2 and Group 3 were comparable. MT was comparable among the groups at date 0, 1, 2, and 3. For the Modified Rankin Scale, at date 3, Groups 1 and 2 had significantly lower scores than Group 3, with no significant difference between Groups 1 and 2.</p> Conclusions <p>Bilateral facilitatory rTMS is an effective and safe intervention for improving swallowing function in PSD.</p>