Low muscle mass is associated with adverse outcomes after surgery. This study examined whether facial muscles, such as the masseter muscle, could be used as a proxy for generalized low muscle mass and could be associated with deviant outcomes after carotid endarterectomy (CEA). As a part of the Vascular Ageing study, patients with an available preoperative CT-scan, who underwent an elective CEA between December 2009 and May 2018, were included. Bilateral masseter muscle area and thickness were measured on preoperative CT scans. A masseter muscle area or thickness of one standard deviation below the sex-based mean was considered low masseter muscle area (LMA) or low masseter muscle thickness (LMT). Of the 123 included patients (73.3% men; mean age 68 (9.7) years), 22 (17.9%) patients had LMA, and 18 (14.6%) patients had LMT. A total of 41 (33.3%) patients had a complicated postoperative course and median length of hospital stay was four (4–5) days. Recurrent stroke within 5 years occurred in eight (6.6%) patients. Univariable analysis showed an association between LMA, complications and prolonged hospital stay. LMT was associated with a prolonged hospital stay (OR 8.78 [1.15–66.85]; p = 0.036) and recurrent stroke within 5 years (HR 12.40 [1.83–84.09]; p = 0.010) in multivariable logistic regression analysis. Masseter muscle might be useful in preoperative risk assessment for adverse short- and long-term postoperative outcomes.