A 76-year-old woman with hypertension was admitted to the hospital with complaints of chest pain and dyspnea. An echocardiogram and pulmonary computed tomography angiography showed right atrial myxoma complicated with pulmonary thromboembolism. An operation to resect the right atrial myxoma and pulmonary embolism was recommended; however, the patient refused and was discharged with anticoagulation therapy. Two years later, she developed dyspnea. Radiological studies and echocardiography showed similar results with the previous findings. The patient underwent mediastinotomy with resection of the right atrial myxoma and pulmonary embolectomy. As there are few reports on right atrial myxoma complicated with pulmonary embolism, we report a successful case of surgical removal of right atrial myxoma and pulmonary embolism.