We discuss the case of a 61-year-old male patient with hypertrophic cardiomyopathy and chest pain on exertion. Coronary angiography and intravascular ultrasound revealed an intermediate stenosis in the proximal site of the left anterior descending artery, while Tc-99m myocardial scintigraphy revealed exercise-induced myocardial ischemia in the anteroseptal wall and apical portion. Flow velocity-derived coronary flow reserve (CFR) and pressure-derived fractional flow reserve (FFRmyo) were both low (1.1 and 0.59), suggesting that the stenosis was functionally significant. Directional coronary atherectomy greatly improved the FFRmyo (0.99), the scintigraphic findings, and anginal pain but did not improve the CFR (1.2). FFRmyo was useful in assessing the functional significance of an equivocal coronary stenosis and its interventional resolution.