Introduction: Pharyngeal residue, defined as the material remaining in the pharynx post-swallow, is a sign of swallowing biomechanical impairment and a clinical predictor of aspiration. This study investigates the correlation between pharyngeal residue severity using the Mansoura FEES Residue Rating Scale (MFRRS) and penetration/aspiration scores using the penetration-aspiration scale (PAS) on FEES. Methods: Two hundred ten (210) swallows were obtained during standard FEES assessments of thirty patients with poststroke dysphagia. Residue, in both vallecula and the pyriform sinuses’ locations, and penetration/aspiration were scored using MFRRS and PAS, respectively. The Spearman’s rank-order correlation was used to assess the correlation between residue and PAS scores. The significance of the obtained results was judged at the (p < 0.05) level. Results: Significant strong positive correlations were demonstrated between PAS scores and each vallecular residue score (rs = 0.663, p = 0.000) and pyriform residue score (rs = 0.688, p = 0.001). Conclusion: There is a significant strong positive correlation between residue severity and penetration/aspiration in each anatomical site evaluated (valleculae and pyriform sinuses). Our results do not designate one site as riskier than the other because either can contribute to aspiration, but rather demonstrate penetration/aspiration to better correlate with the overall severity of the residue, perhaps as a better marker for pharyngeal inefficiency. This study offers insight into the association of residue severity with swallowing safety and efficiency.