Abstract Background Noninvasive fractional flow reserve derived from coronary computed tomography angiography (FFRct) is developed as a decision-making tool in daily clinical practice. However, its diagnostic performance has not been sufficiently explored in patients with severe aortic stenosis (AS). Purpose To identify the diagnostic performance of FFRct in patients with severe AS using invasive fractional flow reserve (FFR) as the reference standard. Methods This study was a retrospective observational that included consecutive patients with severe AS undergoing TAVI who had concomitant intermediate coronary artery stenosis based on preoperative invasive coronary angiography. Preoperative invasive FFR and CT data preoperatively before TAVI were prospectively collected. Results We analyzed the data of patients with severe AS demonstrating intermediate coronary artery stenosis and compared the FFRct values with the invasive FFR values. Among 93 patients (100 vessels), the median FFR and FFRct (Q1, Q3) were 0.85 (0.78, 0.90) and 0.83 (0.72, 0.88), respectively. The FFRct values significantly correlated with the FFR values (r = 0.57; p < 0.0001). The vessel-based analysis of the accuracy of FFRct showed a sensitivity of 90.3%, specificity of 73.9%, positive predictive value of 60.9%, and negative predictive value of 94.4%. Conclusions FFRct demonstrated a significant correlation with invasive FFR and a high negative predictive value in patients with severe AS. These findings suggest that FFRct would be a clinically beneficial noninvasive tool for excluding functional coronary artery stenosis in patients with severe AS.