Swallowing is a sophisticated process involving the precise and timely coordination of the central and peripheral nervous systems, along with the musculatures of the oral cavity, pharynx, and airway. The role of the infratentorial neural structure, including the swallowing central pattern generator and cranial nerve nuclei, has been described in greater detail compared with both the cortical and subcortical neural structures. Nonetheless, accumulated data from analysis of swallowing performance in patients with different neurological diseases and conditions, along with results from neurophysiological studies of normal swallowing have gradually enhanced understanding of the role of cortical and subcortical neural structures in swallowing, potentially leading to the development of treatment modalities for patients suffering from dysphagia. This review article summarizes findings about the role of both cortical and subcortical neural structures in swallowing based on results from neurophysiological studies and studies of various neurological diseases. In sum, cortical regions are mainly in charge of initiation and coordination of swallowing after receiving afferent information, while subcortical structures including basal ganglia and thalamus are responsible for movement control and regulation during swallowing through the cortico-basal ganglia-thalamo-cortical loop. This article also presents how cortical and subcortical neural structures interact with each other to generate the swallowing response. In addition, we provided the updated evidence about the clinical applications and efficacy of neuromodulation techniques, including both non-invasive brain stimulation and deep brain stimulation on dysphagia.