A 10-year-old-girl who underwent Roux-en-Y cystojejunostomy under the diagnosis of choledochal cyst at another hospital at the age of 3 months was referred to our hospital due to abdominal pain. Abdominal ultrasonography (USG) and computed tomography (CT) showed the type I choledochal cyst and multiple gall bladder stones. Severe inflammation and adhesion made difficulty of radical resection and only partial resection of choledochal cyst with Roux-en-Y hepaticojejunostomy could be performed. She complained of intermittent abdominal pain, fever, nausea and vomiting 2 1/2 years after the second operation. Follow-up abdominal CT scan showed the polypoid nodular lesion in the remnant choledochal cyst and suspicious metastatic lesion in the segment 7 of the liver. The duodenum was obstructed by the mass arising from the remnant choledochal cyst. The USG-guided liver biopsy revealed the moderately differentiated adenocarcinoma. A secondary palliative gastrojejunostomy was performed to relieve the obstruction of duodenum. She died of hepatic insufficiency 4 months later of third operation.