We report a case of intrahepatic cholangiocarcinoma arising 33 years after excision of a choledochal cyst. A 61-year-old woman was admitted to our hospital complaining of fever. Thirty-three years ago she had undergone extrahepatic choledochal cystectomy and choledochojejunostomy for a choledochal cyst. Computed tomography showed a tumor in the anterior segment of the liver, extending to the posterior and medial segments and the right portal vein. Intrahepatic biliary stones were seen in the bile ducts. We performed extended right lobectomy. Microscopically, the tumor was cholangiocarcinoma. Most of the tumor area was composed of invasive adenocarcinoma but a carcinoma-in-situ component was also observed in some regions including the hilar bile duct, where an intrahepatic biliary stone was seen. This suggests that the cancer development could be related to intrahepatic cholestasis. Patients with choledochal cyst may have to be carefully followed up for more than 30 years even after diversion surgery.