A rare case of congenital duodenal atresia (DA) associated with a choledochal cyst (CC) is reported. At 38 weeks of gestation, a 1,610-g girl was born by cesarean section with a prenatal diagnosis of DA. After the disorder was confirmed by X-ray, she underwent a duodenoduodenostomy for a complete separation of the duodenum with an annular pancreas. Thirty-two months after the initial operation, she developed upper abdominal pain and acholic stools. Abdominal ultrasonography demonstrated a CC and dilatated intrahepatic bile ducts. Magnetic resonance cholangiopancreatography showed an anomalous arrangement of the choledochus and main pancreatic duct. A diffusely dilatated extrahepatic bile duct was resected, and a hepaticoduodenostomy was performed after cholecystectomy. The patient was discharged without complications. We could not find a similar case report in the English literature. Although it is not reported that there is a close relationship in embryologic development of DA and CC, one should be aware of the possibility of this combination.