Aims: Surgical antimicrobial prophylaxis (SAP) is an important measure to reduce post-operative infections. Guidelines exist, but their efficacy and performance in children is poorly understood compared with adults. To review adherence to SAP guidelines, this study assesses risk factors for non-adherence and rate of early post-surgical infections. Methods: A retrospective cohort study of paediatric surgical cases (0-<18 years) at a tertiary children's hospital was performed. Patient characteristics, surgical factors and antimicrobial details were evaluated against hospital guidelines for overall adherence and domains of: antimicrobial choice, dose, re-dosing, timing and duration. Multiple regression analysis was used to determine risk factors for non-adherence. Hospital records were reviewed for post-operative infections at 7 and 30 days. Results: Among 326 cases, overall guideline adherence was 39.6% but varied by domain and surgical subspecialty. Incorrect wound classification was associated with overall non-adherence on multivariate regression (odds ratio (OR): 2.59; P < 0.001). Incorrect antimicrobial choice was more likely in children with penicillin hypersensitivity (OR 138.34, P = 0.004) and incorrect dosing more likely in adolescent patients (OR 4.33; P = 0.004). Presence of invasive devices was associated with prolonged duration of antimicrobials (OR 2.92, P = 0.016). Only two post-operative infections were documented by 30 days, but data were insufficient to exclude mild infections managed in the community. Conclusions: SAP was suboptimal in children, with areas for improvement including better guidance on wound classification, allergy management and care for adolescent patients. Documented infections were rare, but mild infections were unable to be excluded due to limited postdischarge information.