A 29-year-old woman presented with shortness of breath, vague chest pain, and prominent intermittent ejection systolic murmur. Transthoracic echocardiography showed a large mass in the right ventricular outflow tract. Transesophageal echocardiography demonstrated two masses that were adherent to the tricuspid valve and intermittently prolapsed through the pulmonary valve. Computed tomography of the chest corroborated the echocardiographic findings. Currently, there are no definitive guidelines regarding the optimal management of right heart thrombi in patients with antiphospholipid syndrome. Our patient did not respond to a standard dose of rt-PA used in the treatment of pulmonary embolus. She underwent successful surgical resection of the thrombi without complications.