A 10-year-old-girl was referred to our hospital due to abdominal pain. She underwent Roux-en-Y cystojejunostomy for a choledochal cyst at another hospital at the age of 3 months. Abdominal ultrasonography (USG) and computed tomography (CT) showed type I choledochal cyst and multiple gallbladder stones. Because of severe inflammation and adhesion, partial resection of the choledochal cyst and Roux-en-Y hepaticojejunostomy was performed. Two and one half years later, intermittent abdominal pain, fever, nausea and vomiting occured. Abdominal CT scan showed a polypoid nodular lesion in the remnant of the choledochal cyst and probable metastasis at segment 7 of the liver. The duodenum was obstructed by the mass. Liver biopsy revealed moderately differentiated adenocarcinoma. A palliative gastrojejunostomy was performed to relieve duodenal obstruction. She died of hepatic insufficiency 4 months later.