The aims of this study are to clarify whether discrepancies between angiographic and fractional flow reserve (FFR) measurements (visual–functional mismatch) influence coronary flow profiles after percutaneous coronary intervention. While current guidelines FFR-guided revascularization, clinical practice most commonly relies on angiographic evaluation, which may under- or over-estimate the functional relevance of the lesion. Our retrospective analysis involved 274 vessels from 264 patients with stable angina pectoris who underwent FFR, index of microvascular resistance, and coronary flow reserve (CFR) measurements before and after PCI. Visual–functional concordance and discordance (reverse mismatch) were defined as angiographic stenosis > 50% with FFR ≤ 0.80 and angiographic stenosis ≤ 50% with FFR ≤ 0.80, respectively. Propensity score-matched cohort included 132 lesions (66 lesions: concordant findings, 66 lesions: reverse mismatch). The change in coronary flow profiles after PCI was assessed in terms of FFR, CFR, index of microvascular resistance (IMR), and mean transit time (T_mn). Compared with concordant territories, reverse mismatch territories were associated with lower pre-PCI IMR, higher pre-PCI CFR, greater minimum lumen diameter and smaller reference diameter (all comparisons, P < 0.05). After propensity score matching, the prevalence and extent of coronary flow improvement after PCI, evaluated by CFR and T_mn, were both remained significantly greater in concordant territories (all comparisons, P < 0.05). The prevalence and extent of coronary flow improvement after PCI assessed by the physiologic indices was significantly greater in visual–functional concordant lesions, suggesting that these coronary physiologic changes were associated with discrepancy between angiographic measurements.