Subaortic membrane (SAM) is a discrete fibromuscular structure which causes left ventricular outflow tract obstruction and leads to the symptomatology of valvular aortic stenosis. It is known to be associated with other congenital cardiac defects in around 30% of cases. However, it has not been associated with chronic pulmonary thromboembolism in the past. We present a case of a middle-aged Pakistani man who presented with dyspnea and hemoptysis. He was found to have a SAM and severe pulmonary hypertension on transthoracic echocardiogram. A coronary angiogram revealed non-obstructive left main coronary artery disease. A computed tomography (CT) scan chest was done to evaluate the cause of severe pulmonary hypertension unexplained by SAM which revealed chronic pulmonary thromboembolism. Surgical resection was deferred due to high risk. Hence, he was kept on anticoagulation for pulmonary thromboembolism, and aspirin and a statin for non-obstructive coronary artery disease. Over the course of two months, his symptoms improved. This case highlights the importance of evaluating different causes of pulmonary hypertension in patients with SAM.