Purpose To compare two technical approaches for determination of coronary computed tomography (CT) angiography-derived fractional flow reserve (FFR)-FFR derived from coronary CT angiography based on computational fluid dynamics (hereafter, FFR) and FFR derived from coronary CT angiography based on machine learning algorithm (hereafter, FFR)-against coronary CT angiography and quantitative coronary angiography (QCA). Materials and Methods A total of 85 patients (mean age, 62 years ± 11 [standard deviation]; 62% men) who had undergone coronary CT angiography followed by invasive FFR were included in this single-center retrospective study. FFR values were derived on-site from coronary CT angiography data sets by using both FFR and FFR. The performance of both techniques for detecting lesion-specific ischemia was compared against visual stenosis grading at coronary CT angiography, QCA, and invasive FFR as the reference standard. Results On a per-lesion and per-patient level, FFR showed a sensitivity of 79% and 90% and a specificity of 94% and 95%, respectively, for detecting lesion-specific ischemia. Meanwhile, FFR resulted in a sensitivity of 79% and 89% and a specificity of 93% and 93%, respectively, on a per-lesion and per-patient basis (P = .86 and P = .92). On a per-lesion level, the area under the receiver operating characteristics curve (AUC) of 0.89 for FFR and 0.89 for FFR showed significantly higher discriminatory power for detecting lesion-specific ischemia compared with that of coronary CT angiography (AUC, 0.61) and QCA (AUC, 0.69) (all P < .0001). Also, on a per-patient level, FFR (AUC, 0.91) and FFR (AUC, 0.91) performed significantly better than did coronary CT angiography (AUC, 0.65) and QCA (AUC, 0.68) (all P < .0001). Processing time for FFR was significantly shorter compared with that of FFR (40.5 minutes ± 6.3 vs 43.4 minutes ± 7.1; P = .042). Conclusion The FFR algorithm performs equally in detecting lesion-specific ischemia when compared with the FFR approach. Both methods outperform accuracy of coronary CT angiography and QCA in the detection of flow-limiting stenosis.