Cholelithiasis is a rare but known complication of surgery for duodenal atresia. Occurrence of choledocholithiasis as sequelae of duodenoduodenostomy is still rarer. Biliary stasis resulting from compression of common bile duct due to periductal fibrosis may predispose to gallstone formation. We are reporting a case of choledocholithiasis in a 6 year old child as a late post-operative complication of duodenoduodenostomy (for duodenal atresia in the neonatal period). To the best of our knowledge this is the first case of its kind reported in English literature. Cholecystectomy followed by choledocholithotomy was done and the patient had an uneventful recovery. Upper abdominal pain in any patient with a history of surgery for duodenal atresia in the past warrants a thorough evaluation for any biliary tract anomaly, cholecystitis, cholangitis, cholelithiasis or choledocholithiasis.