Background Perineal reconstruction following salvage APR’s for squamous cell carcinoma of the anus (SCCA) are scant with conflicting results from large and single center studies. We analyzed these techniques taking into account sociodemographic and oncologic variables. Methods This is a retrospective cohort study from 2016-2019 using a targeted ACS/NSQIP database stratified into primary closure (PC), abdominal myocutaneous (AM), lower extremity (LE), and omental pedicled (OP) flaps. We analyzed major and wound complications through univariate and multivariate regression analysis. Results A total of 766 patients were analyzed, 512 (67%) had PC, 196 (25%) AM, 36 (5%) OP and 22 (3%) LE. Rates of chemotherapy and radiation within 90 days were similar between the groups. Having 2 or more additional organs resected was more common for the AM group (AM 4.1%, PC 1.6%, OP 3.3%, LE 0%). Overall, major complication rate was 41% (n = 324). Primary closure had 35.0%, OP 47.2%, AM 52.6%, and LE 45.5%. Wound complication rate was highest in AM with 11.7%, followed by OP 8.3%, PC 5.9%, and LE 0%. The multivariate regression analysis demonstrated none of the closure techniques to be associated with increasing or decreasing the probability of having a major or wound complication. Morbidity probability was the sole predictor of major complication (OR 1.07, 95% CI 1.04-1.1) Conclusions Myocutaneous and omental flaps are associated with comparable wound and major complications when taking into account the baseline, oncologic and perioperative variables that drive the clinical decision making when selecting a perineal reconstruction.