Patients with infratentorial stroke (IS) exhibit more severe dysphagia and a higher risk of aspiration than patients with supratentorial stroke. Nevertheless, a large proportion of patients with IS regain swallowing function within 6 months; however, the neural mechanism for this recovery remains unclear. We aimed to investigate possible neuroplastic changes involved using functional magnetic resonance imaging (fMRI) and their relation to swallowing function. We assessed 21 patients with IS (mean age: 59.9 ± 11.1 years) exhibiting dysphagia in the subacute phase and 21 healthy controls (mean age: 57.1 ± 7.8 years). Patient evaluations were based on the functional oral intake scale (FOIS), videofluoroscopic swallow study (VFSS), and fMRI. Temporal swallowing measures and the penetration-aspiration scale (PAS) were obtained using VFSS. Whole-brain–medulla resting-state functional connectivity (rsFC) was calculated and compared between patients and healthy controls. The rsFCs were also correlated with functional measures within the patient group. In patients with IS, whole-brain–medulla rsFCs were significantly higher in the precuneus, the left and right precentral gyrus, and the right supplementary motor area compared to those in healthy controls (P < 0.001, family-wise error-corrected cluster-level P < 0.05). The rsFCs to the medulla for the left (r = −0.507, P = 0.027) and right side (r = −0.503, P = 0.028) precentral gyrus were negatively correlated with the PAS. The rsFC between the left (r = 0.470, P = 0.042) and right (r = 0.459, P = 0.048) precentral gyrus to the medulla was positively correlated with upper esophageal sphincter opening durations (UOD). In addition, PAS was also correlated with UOD (r = −0.638, P = 0.003) whereas the laryngeal closure duration was correlated with the hyoid bone movement duration (r = 0.550, P = 0.015). Patients with IS exhibited overall modulation of cortical-medulla connectivity during the subacute phase. Patients with higher connectivities showed better swallowing performance. These findings support that there is cortical involvement in swallowing regulation after IS and can aid in determining potential treatment targets for dysphagia.