Functional magnetic resonance imaging (fMRI) has not previously been used to localize the swallowing functional area in repetitive transcranial magnetic stimulation (rTMS) treatment for post-stroke dysphagia; Traditionally, the target area for rTMS is the hotspot, which is defined as the specific region of the brain identified as the optimal location for transcranial magnetic stimulation (TMS). This study aims to compare the network differences between the TMS hotspot and the saliva swallowing fMRI activation to determine the better rTMS treatment site and investigate changes in functional connectivity related to post-stroke dysphagia using resting-state fMRI.