<p>This study aimed to investigate the efficacy of intermittent theta burst stimulation (iTBS) combined with neuromuscular electrical stimulation (NMES) in the treatment of dysphagia after stroke and the changes of brain function.55 participants were randomly assigned to iTBS combined with NMES group (<i>n</i> = 18),iTBS group (<i>n</i> = 18) or NMES group(<i>n</i> = 19). All groups received two-week conventional swallowing therapy.On this basis, the iTBS combined with NMES group received a two-week iTBS combined with NMES treatment, the iTBS group received iTBS combined with sham NMES treatment, the NMES group received sham iTBS combined with NMES treatment. Before and after treatment, Standard Swallowing Function Assessment Scale (SSA), Penetration-Aspiration Scale(PAS), Functional Oral Intake Scale(FOIS), Yale Pharyngeal Residual Severity Scale(YPR-SRS) and swallowing quality of life questionnaire (SWAL-QOL) were used to assess swallowing function. In addition, functional near-infrared spectroscopy was used to investigate participants’ brain function.After treatment, compared with NMES or iTBS group, iTBS combined with NMES group showed significant improvement in SSA, SWAL-QOL, FOIS, PAS, and YPR-SRS scores, increased the activation of Broca (<i>P</i> = 0.033, with FDR corrected) and temporopolar cortex (<i>P</i> = 0.009, with FDR corrected), and improved the functional connectivity between rois.</p>