We report a case of a 50-year-old man with anomalous aortic origin of the right coronary artery (AAORCA) and hypertrophic obstructive cardiomyopathy (HOCM), who was treated with modified unroofing and septal myectomy. The patient presented with exertional syncope. Echocardiography revealed systolic anterior motion (SAM)-associated severe mitral regurgitation (MR) and HOCM. Coronary computed tomography (CT) showed AAORCA with an inter-arterial course and occlusion of the left anterior descending artery (LAD). Intraoperative findings confirmed intramural segment of the anomalous coronary artery was near the commissure of the aortic valve. To preserve native aortic valve function, modified unroofing technique was employed to establish a new right coronary ostium. Septal myectomy was performed to relieve left ventricular outflow tract obstruction, and coronary artery bypass grafting using the left internal thoracic artery was conducted to revascularize the LAD. Postoperatively, myocardial ischemia was resolved, and MR disappeared. The patient was discharged on postoperative day 10 without complications and has remained free of syncope during three years of follow-up.