Purpose: Transcranial direct current stimulation (tDCS) combined with swallowing training might improve swallowing function in patients with post-stroke dysphagia. We investigate the effects of transcranial direct current stimulation (tDCS) combined with swallowing training on post-stroke dysphagia. Methods: Sixteen patients with post-stroke dysphagia, diagnosed using video fluoroscopic swallowing (VFSS), were randomly assigned into two groups: (1) anodal tDCS group (1 mA for 20 min), or (2) sham group (1 mA for 30 s). Patients received anodal tDCS or sham over the pharyngeal motor cortex of the affected hemisphere during 30 min of conventional swallowing training for 10 days. Functional dysphagia scale (FDS) scores based on VFSS were measured at baseline and immediately and 3 months after the intervention. The effect of tDCS on dysphagia was analyzed using a generalized linear model (GLM) with repeated measures. Results: After the intervention, FDS scores improved in both groups without significant differences. However, 3 months after the intervention, anodal tDCS elicited greater improvement in terms of FDS compared to the sham group (β = −7.79, p = 0.041) after controlling for age, National Institutes of Health Stroke Scale (NIHSS) score, lesion size, baseline FDS score, and time from stroke onset. Conclusions: Anodal tDCS applied over the affected pharyngeal motor cortex can enhance the outcome of swallowing training in post-stroke dysphagia. Our results suggest that non-invasive cortical stimulation has a potential role as an adjuvant strategy during swallowing training in patients with post-stroke dysphagia.