Dysphagia is a largely inevitable symptom in both progressive supranuclear palsy (PSP) and Parkinson’s disease (PD). To date, comparative studies in these diseases have failed to detect differences in the severity of impairments in swallowing safety or efficiency, potentially due to small sample sizes and outcome measures with low sensitivity. Therefore, this study sought to address these limitations by using novel measurement methodology to comprehensively compare swallowing safety and efficiency impairments between these populations in order to better understand whether differences may exist and guide clinical management. Twenty-four participants with PSP and 24 with PD were matched for disease duration and completed flexible endoscopic evaluations of swallowing. A visual analog scale and penetration-aspiration scale quantified swallowing safety and efficiency. Bayesian multilevel models compared the frequency, severity, and variability of swallowing impairments. Individuals with PSP demonstrated greater impairments in swallowing safety, including deeper and more variable airway invasion and more frequent vocal fold and subglottic residue. Swallowing efficiency was also more impaired among individuals with PSP, including more frequent hypopharyngeal residue (with solids) and more severe residue in the oropharynx (with thin liquids and solids) and hypopharynx (with thin liquids). When airway or pharyngeal residue was present, similar within-subject variability of the amount of residue was appreciated across anatomic landmarks. This is the first study comparing the frequency, severity, and variability of swallowing impairments between PSP and PD populations. Our findings demonstrate more pronounced impairments in swallowing safety and efficiency for PSP compared to PD. These findings provide a clinically relevant characterization of swallowing measures using novel methodological and statistical approaches attempting to resolve some limitations of prior studies.