We report a case of intrahepatic cholangiocarcinoma with biliary lithiasis arising 47 years after surgery for a congenital biliary dilatation (CBD). A 62-year-old woman was admitted for the investigation of a liver tumor. She had undergone a choledochoduodenostomy at the age of 15 years for CBD and resection of an extrahepatic bile duct with choledochojejunostomy because of cholangitis at the age of 55 years. An enhanced computed tomography (CT) revealed a liver tumor 50 mm in diameter in the S6 region with surrounding lymph node swelling and intrahepatic metastatic lesions in the S8 region. A drip infusion cholangiographic CT showed biliary lithiases in the left liver. An extended right hepatectomy and lymph node dissection was considered but was abandoned because of suspicions of liver functional insufficiency as a result of biliary lithiasis. She underwent biliary lithotomy through a percutaneous transhepatic cholangioscopy and subsequent systemic chemotherapy.