Purpose <p>Laparoscopic surgery has been accepted as an effective and safe approach for the treatment in pediatric choledochal cysts (CDCs). However, bile leakage remains one of the most severe early postoperative complications. This study aims to identify risk factors for bile leakage following laparoscopic cyst excision and hepaticojejunostomy in pediatric CDCs and optimize perioperative management strategies.</p> Methods <p>A retrospective study was conducted on children who underwent laparoscopic cyst excision and hepaticojejunostomy at Fujian Children’s Hospital between January 2016 and January 2025. Comprehensive clinical data were extracted from institutional electronic medical records. Participants were stratified into bile leakage and non-bile leakage groups. Univariate analysis and multivariate regression models were used to identify risk factors.</p> Results <p>A total of 131 patients were included in this study. The median age of included children was 1.8&#xa0;years (range: 0.1 ~ 14.3), with a male-to-female ratio of 1.0:3.6. There were 14 cases included in the bile leakage groups, with 7 cases (50%) required surgical reintervention. Univariable analysis indicated that bile leakage was associated with preoperative pancreatitis (<i>p</i> = 0.02), cholangitis (<i>p</i> = 0.03), type IV CDCs (<i>p</i> = 0.03), bile duct stones (<i>p</i> = 0.01), and prior biliary surgery (p = 0.02). Multivariable analysis showed that bile duct stones (OR = 4.4, 95% CI 1.0 ~ 18.8) and prior biliary surgery (OR = 5.1, 95% CI 1.1 ~ 23.0) were independent factors that were associated with bile leakage.</p> Conclusion <p>Bile duct stones and prior biliary surgery significantly increase the risk of bile leakage in pediatric CDCs following laparoscopic cyst excision and hepaticojejunostomy. Proactive management of biliary inflammation, complete stone clearance, and meticulous surgical techniques are critical for the prevention of complications.</p>