To explore rehabilitation options for dysphagia induced by Coronavirus disease 2019 (COVID-19) in post-stroke patients. Methods: A patient with post-stroke sequelae who developed COVID-19-induced dysphagia for more than one month underwent a two-stage comprehensive assessment and treatment. In the first stage, intermittent theta burst stimulation (iTBS) to the bilateral swallowing cortex, balloon dilation therapy, and standard swallowing rehabilitation exercise were performed five times per week for two weeks. In the second stage, iTBS was applied to the suprahyoid muscles for an additional two weeks. Assessments were performed before treatment (T0), after the first stage (T1) and after the second stage (T2). The assessment indicators included the Standardized Swallowing Assessment (SSA), Yale Pharyngeal Residue Severity Rating Scale (YPR-SRS) and Penetration-Aspiration Scale (PAS) based on Flexible Endoscopic Evaluation of Swallowing (FEES), Functional Oral Intake Scale (FOIS), Motor Evoked Potentials (MEP) of suprahyoid muscles, and Functional Near-Infrared Spectroscopy (fNIRS). Results: Compared with T0, there was no significant improvement in swallowing function at the end of T1, with moderate to severe residue observed in the epiglottic vallecula and pyriform sinus. The patient could only attempt minimal liquid intake. Compared with the end of T1, the patient's swallowing function was significantly improved at the end of T2, with the SSA score decreasing from 32 to 22. YPR-SRS improved from moderate/severe residue to mild/trace residue, the PAS score decreased from 4 to 1, and the FOIS increased from 2 to 6. The patient could consume food orally with the exception of large gulps. The MEP latency reduced, and the amplitude increased in the bilateral suprahyoid muscles. The fNIRS results revealed a significant increase in the functional connectivity of the cortical swallowing network. Conclusion: iTBS to the suprahyoid muscles and bilateral swallowing cortex combined with balloon dilation is a safe and effective rehabilitation therapy for treating post-COVID-19 dysphagia in post-stroke patients, potentially by improving the function of the supraglottic muscles and increasing the excitability of swallowing-associated cortical areas and functional connectivity of brain networks.