Repetitive transcranial magnetic stimulation to the pharyngeal motor cortex has shown beneficial effects on poststroke dysphagia. Previous studies, however, using intermittent theta burst stimulation (iTBS) for dysphagia have targeted the suprahyoid motor cortex. This study aimed to investigate the effects of iTBS to the pharyngeal motor cortex in patients with poststroke dysphagia, using ultrasound and videofluoroscopic swallowing studies (VFSS). A randomized controlled trial was conducted on patients with dysphagia due to a first-time unilateral stroke. Patients who had signs and symptoms of dysphagia and showed aspiration or penetration on VFSS were included. Twenty-eight patients were randomly assigned to either real or sham iTBS groups, and each patient underwent five sessions of iTBS to the ipsilesional pharyngeal motor cortex. Each iTBS session was followed by conventional dysphagia treatment for 30 min. The hyoid–larynx approximation measured by ultrasound, penetration–aspiration scale (PAS) and functional dysphagia scale (FDS) assessed by VFSS were evaluated before and after completion of iTBS. There were no significant differences between the two groups in terms of demographic and clinical characteristics, including age and type of stroke. The hyoid–larynx approximation ratio increased in the real iTBS group and decreased in the sham iTBS group (median values of pre–post differences were 0.27 vs. −0.01, P