Background: Coronary CT angiography with noninvasive fractional flow reserve (FFR) predicts lesion-specific ischemia when compared with invasive FFR. The longer term prognostic value of CT-derived FFR (FFRCT) is unknown. Purpose: To determine the prognostic value of FFRCT when compared with coronary CT angiography and describe the relationship of the numeric value of FFRCT with outcomes. Materials and Methods: This prospective subanalysis of the NXT study (Clinicaltrials.gov: NCT01757678) evaluated participants suspected of having stable coronary artery disease who were referred for invasive angiography and who underwent FFR, coronary CT angiography, and FFRCT. The incidence of the composite primary end point of death, myocardial infarction, and any revascularization and the composite secondary end point of major adverse cardiac events (MACE: cardiac death, myocardial infarction, unplanned revascularization) were compared for an FFRCT of 0.8 or less versus stenosis of 50% or greater on coronary CT angiograms, with treating physicians blinded to the FFRCT result. Results: Long-term outcomes were obtained in 206 individuals (age, 64 years 6 9.5), including 64% men. At median follow-up of 4.7 years, there were no cardiac deaths or myocardial infarctions in participants with normal FFRCT. The incidence of the primary end point was more frequent in participants with positive FFRCT compared with clinically significant stenosis at coronary CT angiography (73.4% [80 of 109] vs 48.7% [91 of 187], respectively; P , .001), with the majority of outcomes being planned revascularization. Corresponding hazard ratios (HRs) were 9.2 (95% confidence interval [CI]: 5.1, 17; P , .001) for FFRCT and 5.9 (95% CI: 1.5, 24; P = .01) for coronary CT angiography. FFRCT was a superior predictor compared with coronary CT angiography for primary end point (C-index FFRCT, 0.76 vs coronary CT angiography, 0.54; P , .001) and MACE (FFRCT, 0.71 vs coronary CT angiography, 0.52; P = .001). Frequency of MACE was higher in participants with positive FFRCT compared with coronary CT angiography (15.6% [17 of 109] vs 10.2% [19 of 187], respectively; P = .02), driven by unplanned revascularization. MACE HR was 5.5 (95% CI: 1.6, 19; P = .006) for FFRCT and 2.0 (95% CI: 0.3, 14; P = .46) for coronary CT angiography. Each 0.05-unit FFRCT reduction was independently associated with greater incidence of primary end point (HR, 1.7; 95% CI: 1.4, 1.9; P , .001) and MACE (HR, 1.4; 95% CI: 1.1, 1.8; P , .001). Conclusion: In stable patients referred for invasive angiography, a CT-derived fractional flow reserve (FFRCT) value of 0.8 or less was a predictor of long-term outcomes driven by planned and unplanned revascularization and was superior to clinically significant stenosis on coronary CT angiograms. Additionally, the numeric value of FFRCT was an independent predictor of outcomes.