We investigated the functional changes in swallowing and voluntary coughing before and after tracheostomy decannulation among stroke patients who had undergone a tracheostomy. We also compared these functions between stroke patients who underwent tracheostomy tube removal and those who did not within 6 months of their stroke. Seventy-seven stroke patients who had undergone a tracheostomy were enrolled. All patients were evaluated by videofluoroscopic swallowing studies and a peak flow meter through the oral cavity serially until 6 months after their stroke. During the intensive rehabilitation period, if a patient satisfied the criteria for tracheostomy tube removal, the tube was removed. The patients were divided into the ‘decannulated’ group and the ‘non-decannulated’ group according to their tracheostomy tube removal status. In the decannulated group, swallowing function did not change before and after tracheostomy decannulation; however, cough function was significantly improved after decannulation. Although both groups exhibited functional improvement in swallowing and coughing over time, the improvement in the decannulated group was more significant than the improvement in the non-decannulated group. Our results revealed that stroke patients who had better functional improvement in swallowing and coughing were more likely to be potential candidates for tracheostomy decannulation. Stroke patients who recovered from neurogenic dysphagia, they were no longer affected by the mechanical effect of the tracheostomy tube on swallowing function. This study suggests that if patients show improvement in swallowing and coughing after their stroke, a multidisciplinary approach to tracheostomy decannulation would be needed to achieve better rehabilitation outcomes.