We report a 66-year-old man with diffuse bile duct carcinoma arising in a choledochal cyst, who underwent right portal venous branch embolization to minimize the hepatic deficit that would result from extended right lobectomy. After recovery of liver function parameters, extended right lobectomy with caudate lobectomy and pancreatoduodenectomy together with lymphadenectomy and total resection of the extrahepatic bile duct were performed. Currently, there is no evidence of recurrence 24 months after surgery. To our knowledge, this is the first report of resection of a diffuse bile duct carcinoma arising in a choledochal cyst with hepatopancreatoduodenectomy. Surgical issues related to advanced biliary malignancy are also discussed.