Choledochal cyst, also referred to as cystic dilatation of the extrahepatic bile duct, is a rare malformation most frequently seen in female. Malignant changes in choledochal cyst have frequently been described, but only one case of malignant change in childhood has been reported till now. Recently, we experienced a case of bile duct cancer arising in choledochal cyst in a 13-year-old girl. She had been complaining of right upper abdominal pain for 15 days. Abdominal CT scan and ERCP showed a cylindrical dilatation of extrahepatic bile duct with irregular cystic wall mass and multiple liver metastasis which was confirmed as adenocarcinoma by ultrasono-guided needle biopsy. Anomalous pancreaticobiliary ductal union was not seen. This patient was the youngest case of bile duct carcinoma arising in choledochal cyst in Korea.