ObjectiveBranchial cleft cysts present at varying ages; sometimes excision is delayed because of concern about operating in small children. Our goal was to determine if outcomes and complications differed among pediatric age groups. Study designRetrospective, cross-sectional. SettingAmerican College of Surgeons’ National Surgical Quality Improvement Pediatric database. MethodsPatients who underwent a branchial cleft cyst excision between 2016 and 2020 were identified in the American College of Surgeons National Surgical Quality Improvement Program (ACS NSQIP) Pediatric database. Patients with CPT code 42,815: ‘excision branchial cleft cyst, vestige, or fistula, extending beneath subcutaneous tissues and/or into the pharynx’ as their primary procedure were included. Variables of interest included patient demographics, comorbidities, pre-operative risk factors and complications. Results2267 patients with median age of 3.9 (IQR: 7.4, range: 0.04–17.9) years were included. The most common pre-operative risk factors were 149 (7 %) patients with prematurity, 136 (6 %) with developmental delay, 135 (6 %) with congenital malformation, and 128 (6 %) with open wound or wound infection. 68 (3 %) patients experienced at least one post-operative complication, with 73 post-operative complications documented in total. Surgical site infections were the most common complications with 49 (67.1 %) superficial infections, 11 (15.1 %) deep infections, and 4 (5.5 %) organ/space infections. Surgical site infections were the most common reason for related readmission. Duration of anesthesia and operative time increased significantly as patient age increased (p < .001 for both). There was no significant correlation between age and complication incidence. ConclusionBranchial cleft cyst excision is a relatively safe operation with a low complication rate, even in young pediatric populations.