Background: Computed tomography derived Fractional Flow Reserve (CT-FFR) has been shown to decrease the referral rate for invasive coronary angiography (ICA). The purpose of the study was to evaluate the diagnostic performance of CT-FFR compared to hyperemia-free index Resting Full-cycle Ratio (RFR) in patients with relevant aortic stenosis (AS) and intermediate coronary stenosis. Methods: 41 patients with 46 coronary lesions underwent ICA with quantitative coronary angiography (QCA), pressure wire assessment and routine pre-transcatheter aortic valve replacement (TAVR) computed tomography (CT). CT-FFR analysis was performed using prototype on-site software. Results: RFR showed a significant correlation with CT-FFR (Pearson’s correlation, r = 0.632, p < 0.001). On a per-lesion basis, diagnostic accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of CT-FFR were 82.6% (95% CI 68.6–92.2), 69.6% (95% CI 47.1–86.8), 95.7% (95% CI 78.1–99.9), 94.1% (95% CI 69.8–99.1), and 75.9% (95% CI 62.7–85.4), respectively. The optimal cutoff value of the CT-FFR for RFR ≤ 0.89 prediction was 0.815. The area under the receiver curve showed a larger area under the curve for CT-FFR (0.87; 95% CI 0.75–0.98) compared with CTA stenosis of ≥50% (0.54, 95% CI 0.38–0.71), CTA ≥ 70% (0.72, 95% CI 0.57–0.87) and QCA ≥ 50% (0.67, 95% CI 0.52–0.83). Conclusions: CT-FFR assessed by routine pre-TAVR CT is safe and feasible and shows a significant correlation with RFR in patients with AS. CT-FFR is superior to QCA ≥ 50%, CT ≥ 50% and CT ≥ 70% in assessing the hemodynamic relevance of intermediate coronary lesions. Thus, CT-FFR has the potential to guide revascularization in patients with AS.