Obstruction of the bile duct owing to the direct extension of a tumor is occasionally found in patients with a hepatic neoplasm, but bile duct tumor thrombus caused by the intrabiliary transplantation of a free-floating tumor is a rare complication of hepatocellular carcinoma A 50-year-old woman was diagnosed with HCC with bile duct tumor thrombi. She received transarterial chemoembolization (TACE) because her liver function was not suitable for surgery at the time of diagnosis. After TACE, infected biloma occurred recurrently. Thus, resection of the HCC, including the bile duct tumor thrombi, was performed. Six months after the surgery, recurred HCC in the distal common bile duct as drop metastasis was noted. The patient was treated with tomotherapy and has been alive for three years as of this writing, without recurrence. The prognosis of HCC with bile duct tumor thrombi is considered dismal, but if appropriate procedures are selected and are actively carried out, long-term survival can occasionally be achieved.