Dysphagia following stroke is one of the main causes of infection and death in stroke patients. Identifying changes in the structural and functional brain regions associated with post-stroke dysphagia can aid in early screening and clinical intervention. Functional magnetic resonance imaging (fMRI) is widely used in the study of dysphagia after stroke. This review summarizes the research on fMRI imaging of post-stroke dysphagia, focusing on the applications of resting-state fMRI and task-based fMRI in dysphagia, as well as their roles in evaluating the efficacy of various rehabilitation training methods for dysphagia.