Anomalous aortic origin of a coronary artery (AAOCA) is the second most common cause of sudden cardiac death in young athletes. One of the hypothesized mechanisms of ischemia in these patients is the lateral compression of the anomalous artery with an intramural or interarterial course. The presence of a narrowing in the anomalous artery will cause physiologic changes in downstream resistance that should be included for computational assessment of possible clinical ramifications. In this study, we created different compression levels, i.e., proximal narrowing, in the intramural course of a representative patient model and calculated hyperemic stenosis resistance (HSR) as well as virtual fractional flow reserve (vFFR). Models also included the effect of the distal hyperemic microvascular resistance (HMR) on vFFR. Our results agreed with similar FFR studies indicating that FFR is increased with increasing HMR and that different compression levels could have similar FFR depending on the HMR. For example, vFFR at HSR: 1.0–1.3 and HMR: 2.30 mmHg/cm/s is 0.68 and close to vFFR at HSR: 0.6–0.7 and HMR: 1.6 mmHg/cm/s, which is 0.7. The current findings suggest that functional assessment of anomalous coronary arteries through FFR should consider the vascular resistance distal to the narrowing in addition to the impact of a proximal narrowing and provides computational approaches for implementation of these important considerations.