Hepatocellular carcinoma (HCC) rarely presents as an intraductal tumor with no parenchymal lesions. Here, we present a case of HCC arising from an intrahepatic bile duct. A 74-year-old man who had been treated with direct-acting antiviral therapy for hepatitis C virus infection was referred to our hospital because of elevated serum prothrombin levels induced by vitamin K absence II (PIVKA-II). Initial imaging revealed no findings suspicious of HCC; however, repeat CT six months later revealed dilation of the intrahepatic bile ducts in the lateral segment of the liver. Cholangiography revealed a significant stricture of B3, and biopsy suggested adenocarcinoma. A left hepatectomy was performed with a preoperative diagnosis of intrahepatic cholangiocarcinoma. Although a surface nodule on the lateral segment of the liver, suspicious for intrahepatic metastasis, was found intraoperatively, radical resection was performed. Histopathological examination revealed a tumor filling the intrahepatic bile duct from the stump to the peripheral bile duct, with no infiltration into the liver parenchyma. The surface nodule is a dilated peripheral bile duct filled with a tumor with no extrabiliary invasion. Immunohistochemistry suggested HCC. No tumor lesions were observed in the hepatic parenchyma, and the tumor was finally diagnosed as HCC stemming from the biliary epithelium.