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Background: Choledochal cysts are rare congenital anomalies of the biliary tree that may lead to obstruction, chronic inflammation, infection, and malignancy. There is wide variation in the timing of resection, operative approach, and reconstructive techniques. Outcomes have rarely been compared on a national level. Methods: We queried the Pediatric National Surgical Quality Improvement Program (NSQIP) to identify patients who underwent choledochal cyst excision from 2015 to 2020. Patients were stratified by hepaticoduodenostomy (HD) versus Roux‐en‐Y hepaticojejunostomy (RNYHJ), use of minimally invasive surgery (MIS), and age at surgery. We collected several outcomes, including length of stay (LOS), reoperation, complications, blood transfusions, and readmission rate. We compared outcomes between cohorts using nonparametric tests and multivariate regression. Results: Altogether, 407 patients met the study criteria, 150 (36.8%) underwent RNYHJ reconstruction, 100 (24.6%) underwent MIS only, and 111 (27.3%) were less than one year old. Patients who underwent open surgery were younger (median age 2.31 vs. 4.25 years, p = 0.002) and more likely underwent RNYHJ reconstruction (42.7% vs. 19%, p = 0.001). On adjusted analysis, the outcomes of LOS, reoperation, transfusion, and complications were similar between the type of reconstruction, operative approach, and age. Patients undergoing RNYHJ had lower rates of readmission than patients undergoing HD (4.0% vs. 10.5%, OR 0.34, CI [0.12, 0.79], p = 0.02). Conclusions: In children with choledochal cysts, most short‐term outcomes were similar between reconstructive techniques, operative approach, and age at resection, although HD reconstruction was associated with a higher readmission rate in this study. Clinical decision‐making should be driven by long‐term and biliary‐specific outcomes. [ABSTRACT FROM AUTHOR]