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 congenital DA. After the disease was confirmed by radiographs, she underwent a duodenoduodenostomy for 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 dilated intrahepatic bile ducts. Magnetic resonance cholangiopancreatography showed an anomalous arrangement of the choledochus and the main pancreatic duct. A diffusely dilated extrahepatic bile duct was resected, and a hepaticoduodenostomy was performed after a 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 relation of DA and CC in embryologic development, the presence of this combination should be considered.