Cardiac tumors are rare, which were found in only 0.001%–0.300% of cases in a relatively recently reported autopsy series. Among cardiac tumors, primary hemangioma accounted for approximately 2.8% of all primary resected tumors, indicating that this is a particularly rare benign neoplasm. We presented a patient with a 5×3×2 cm cavernous hemangioma arising from the right atrial roof, occupying the atrial septum and inseparable from the aortic root. We successfully performed complete surgical tumor resection and reconstruction of the right atrium and atrial septum using a bovine pericardial patch for a huge cavernous cardiac hemangioma filling the cardiac atrium.