A previously healthy nine-year-old boy with anomalous aortic origin of the left coronary artery (AAOLCA) with high-risk anatomy demonstrated negative stress on magnetic resonance imaging. Invasive cardiac catheterization for intracoronary flow measurement was performed and demonstrated compromised coronary flow during pharmacologic stress and significant stenosis on angiography. The patient underwent surgical intervention with normalization of coronary flow upon postoperative evaluation. Invasive intracoronary flow determination with angiography under provocative stress is emerging as a critical data point for risk stratification and management decision-making in high-risk AAOLCA patients with negative noninvasive perfusion studies.