BACKGROUND: Coronary computed tomography angiography (CTA)-derived fractional flow reserve (FFR) serves as a gatekeeper to invasive coronary angiography (ICA), but its accuracy depends on image quality of the scan. Photon-counting coronary computed tomography angiography (PCCTA) technology enables spectral standard resolution (SR) and ultrahigh resolution (UHR) imaging. OBJECTIVES: This study aims to perform the first intraindividual comparison of SR-PCCTA-derived FFR, UHR-PCCTA-derived FFR, and invasive FFR. METHODS: Between February 2023 and April 2025, 32 patients with a clinical indication for ICA underwent research PCCTA with both SR and UHR acquisitions before ICA. Invasive FFR of intermediate coronary stenoses was measured. SR-PCCTA- and UHR-PCCTA-derived FFR were computed using an on-site, machine-learning-based prototype and compared with invasive FFR. Subanalyses were conducted in severely calcific and diffusely diseased vessels. Diagnostic accuracy for predicting invasive FFR <0.80 of SR-PCCTA- and UHR-PCCTA-derived FFR and concordance in hemodynamic significance classification (<0.80, ≥0.80) were assessed. RESULTS: Invasive FFR, SR-PCCTA-, and UHR-PCCTA-derived FFR were available for 54 vessels. Both SR-PCCTA-derived (ρ: 0.490; P < 0.001) and UHR-PCCTA-derived FFR (ρ: 0.728; P < 0.001) correlated well with invasive FFR. Unlike SR-PCCTA, UHR-PCCTA-derived FFR maintained its correlation in severely calcific (ρ: 0.577; P = 0.039) and diffusely diseased vessels (ρ: 0.772; P = 0.009). UHR-PCCTA-derived FFR outperformed SR-PCCTA in diagnostic accuracy (AUC: 0.93 vs 0.80; P for comparison = 0.012) and hemodynamic significance classification (Cohen's κ: 0.70 vs 0.50). CONCLUSIONS: Both SR-PCCTA- and UHR-PCCTA-derived FFR correlated with invasive FFR, but UHR-PCCTA outperformed SR-PCCTA in diagnostic accuracy and hemodynamic significance classification.