Polycythemia vera (PV) is associated with an increased risk of thrombosis at unusual sites. We report a 53-year-old woman with PV and atrial septal defect (ASD), who presented with the symptoms of right heart failure. Transthoracic echocardiography showed multiple thrombi in the right ventricle and pulmonary artery, which were further confirmed by a helix lung computed tomography scan. The patient was successfully treated with anticoagulation, ASD closure, and inferior vena cava filter.