Swallowing is considered a three-phase mechanism involving the oral, pharyngeal, and esophageal phases. The pharyngeal phase relies on highly coordinated movements in the pharynx and larynx to move food through the aerodigestive crossing. While the brainstem has been identified as the primary control center for the pharyngeal phase of swallowing, existing evidence suggests that the higher brain regions can contribute to controlling the pharyngeal phase of swallowing to match the motor response to the current context and task at hand. This suggests that the pharyngeal phase of swallowing cannot be exclusively reflexive or voluntary but can be regulated by the two neural controlling systems, goal-directed and non-goal-directed. This capability allows the pharyngeal phase of swallowing to adjust appropriately based on cognitive input, learned knowledge, and predictions. This paper reviews existing evidence and accordingly develops a novel perspective to explain these capabilities of the pharyngeal phase of swallowing. This paper aims (1) to integrate and comprehend the neurophysiological mechanisms involved in the pharyngeal phase of swallowing, (2) to explore the reflexive (non-goal-directed) and voluntary (goal-directed) neural systems of controlling the pharyngeal phase of swallowing, (3) to provide a clinical translation regarding the pathologies of these two systems, and (4) to highlight the existing gaps in this area that require attention in future research. This paper, in particular, aims to explore the complex neurophysiology of the pharyngeal phase of swallowing, as its breakdown can lead to serious consequences such as aspiration pneumonia or death.