In patients with antiphospholipid syndrome (APS), thromboembolism and pulmonary hypertension are the most common pulmonary manifestations. Thrombotic obstruction at the level of the main and/or proximal pulmonary arteries is rare. We report a 40-year-old woman without any history of previous arterial and/or venous thrombosis who presented with severe dyspnea and was found to have pulmonary hypertension and positivity for anticardiolipin antibodies. Computed tomography revealed pulmonary truncus thrombosis extending to both right and left pulmonary arteries. The patient and her family refused surgical treatment. She had a prolonged hospital course, was unresponsive to thrombolytic, anticoagulant, antiplatelet, and immunosuppressive treatments, and died of right ventricle and respiratory failure 5 weeks later. This is the first reported case with thrombosis of pulmonary truncus and main pulmonary arteries concurrent with APS.