We report a rare case of hepatolithiasis, which was diagnosed as hilar cholangiocarcinoma and treated with hepatectomy and extrahepatic bile duct resection. A 59-year-old woman presented to a local hospital with liver dysfunction. Diagnostic imaging revealed a biliary stricture at the hepatic hilum and middle bile duct. Hilar cholangiocarcinoma was diagnosed, and she was referred to our hospital for definitive surgical treatment. She underwent left hepatic trisectionectomy, total caudate lobectomy, and extrahepatic bile duct resection. Gross examination of the resected specimen revealed intrahepatic stones firmly adherent to the bile duct wall. Pathological examination revealed no malignant lesions. The epithelium of the bile duct was absent underneath the stone, and the boundary between the stone and bile duct wall was ill defined. To our knowledge, this is the first case report of hepatolithiasis with a biliary stricture caused by peculiar stone formation, mimicking hilar cholangiocarcinoma.