Abstract Introduction A choledochal malformation (CM) is a rare entity, especially in the Western world. We aimed to determine the incidence of CM in the Netherlands and the outcome of surgery for CM in childhood. Methods All pediatric patients who underwent a surgical procedure for type I–IV CM between 1989 and 2014 were entered into the Netherlands Study group on choledochal cyst/malformation. Patients with type V CM were excluded from the present analysis. Symptoms, surgical details, short‐term (<30 days) and long‐term (>30 days) complications were studied retrospectively. Results Between January 1989 and December 2014, 91 pediatric patients underwent surgery for CM at a median age of 2.1 years (0.0–17.7 years). All patients underwent resection of the extrahepatic biliary tree with restoration of the continuity via Roux‐en‐Y hepaticojejunostomy. Twelve patients (12%) were operated laparoscopically. Short‐term complications, mainly biliary leakage and cholangitis, occurred in 20 patients (22%), without significant correlations with weight or age at surgery or surgical approach. Long‐term postoperative complications were mainly cholangitis (13%) and anastomotic stricture (4%). Eight patients (9%) required radiological intervention or additional surgery. Surgery before 1 year of age (OR 9.3) and laparoscopic surgery (OR 4.4) were associated with more postoperative long‐term complications. We did not observe biliary malignancies during treatment or follow‐up. Conclusion Surgery for CM carries a significant short‐ and long‐term morbidity. Given the low incidence, we would suggest that (laparoscopic) hepatobiliary surgery for CM should be performed in specialized pediatric surgical centers with a wide experience in laparoscopy and hepatobiliary surgery.