We report a rare case of intrahepatic cholangiocarcinoma (IHCC) arising many years after excision of a type IV-A congenital choledochal cyst. A 44-year-old man was transferred to our hospital with acute cholangitis more than 34 years after several operations for congenital biliary dilatation. Imaging showed a huge tumor in the left medial section of the liver, extending to the porta hepatis. Although he had no jaundice, the intrahepatic bile ducts showed cylinder-like dilatation with narrowing of the hilar bile duct. At surgery, the tumor was found to arise from the dilated intrahepatic bile duct just above the narrow portion. He underwent a left hepatic trisectionectomy with a vascular procedure. Microscopically, the tumor was confirmed to be moderate-to-well-differentiated tubular adenocarcinoma. Thus, when the narrow segment is left untouched, careful long-term follow-up is important to detect new lesions at an early stage.