Anomalous aortic origin of a coronary artery (AAOCA) is a congenital malformation of the coronary arteries that includes several subtypes. It is a leading cause of sudden cardiac death in young people, especially in competitive athletes. An accurate diagnosis and identification of high-risk patients with AAOCA for referral for surgical repair can help in the management of these patients. However, current diagnostic tools such as invasive angiography, echocardiography, and intravascular ultrasound have known limitations in visualizing coronary orifices and characterizing vessels. In this case report, we report on a 14-year-old adolescent who suffered from repeated incidents of syncope during exercise. Using the computed tomographic fractional flow reserve (CT-FFR) technique, we diagnosed AAOCA, which revealed that his left coronary artery (LCA) originated from the right sinus of Valsalva and ran between the aorta and the pulmonary artery with an intra-arterial wall course (∼20 mm in length), with an abnormal FFR of the LCA at rest. The patient was referred for undergoing unroofing surgery, and the results of repeat CT-FFR showed a significantly improved FFR of the LCA. The patient resumed his normal physical activities without the recurrence of syncope. In this report, we highlight the usefulness of CT-FFR as a non-invasive, feasible, and effective tool to guide whether a patient with AAOCA requires surgical revascularization and to evaluate the effectiveness of the procedure after surgery.