Background: Hepatocellular carcinoma (HCC) with tumor thrombus (TT) extending into the right atrium (RA) is rare, and most cases are at an advanced stage with a poor prognosis. We report a case of HCC with TT in the RA (RATT) with 15-year survival.Case presentation: The patient was a 67-year-old man with a huge HCC with RATT. He developed edema of the lower extremities in November 2002. Then, a liver tumor 6.5 cm in diameter in hepatic segments 7 and 8 was identified by ultrasonography and computed tomography. Cavo-atrial thrombectomy was performed successfully using cardiopulmonary bypass (CPB) with heparinization and cardiac arrest. After the thrombectomy, right hepatectomy was performed using the hanging maneuver. The right hepatic vein was transected, and the stump was closed with a running suture. The total operation time was 10 h 48 min, and the total blood loss was 7267 mL. The patient recovered uneventfully except for right pleural effusion, and he experienced no side effects related to CPB, such as immunosuppression or cerebral infarction. He was cancer-free for approximately 9 years after the surgery. A new lesion in the remnant liver was detected by magnetic resonance imaging in March 2012. He underwent six rounds of transcatheter arterial chemoembolization, followed by sequential administration of sorafenib and sunitinib. Radiation therapy was administered to the remnant liver twice and to the spine after he was diagnosed with bone metastasis. Finally, the patient died 6 years after the recurrence. Conclusions: Cavo-atrial thrombectomy under CPB prior to hepatectomy for HCC with RATT can be performed safely to prevent major complications related to CPB. Our patient’s postoperative clinical course followed by multidisciplinary therapies led to an approximately 15-year survival.