Quantitative flow ratio (QFR) and fractional flow reserve (FFR) have not yet been compared head to head with perfusion imaging as reference for myocardial ischemia. We aimed to compare the diagnostic accuracy of QFR and FFR with myocardial perfusion scintigraphy (MPS) or cardiovascular magnetic resonance (CMR) as reference. This study is a predefined post hoc analysis of the Dan-NICAD study (NCT02264717). Patients with suspected coronary artery disease by coronary computed tomography angiography (CCTA) were randomized 1:1 to MPS or CMR and were referred to invasive coronary angiography with FFR and predefined QFR assessment. Paired data with FFR, QFR and MPS or CMR were available for 232 vessels with stenosis in 176 patients. Perfusion defects were detected in 57 vessel territories (25%). For QFR and FFR the diagnostic accuracy was 61% and 57% (p = 0.18) and area under the receiver operating curve was 0.64 vs. 0.58 (p = 0.22). Stenoses with absolute indication for stenting due to diameter stenosis > 90% by visual estimate were not classified as significant by either QFR or MPS/CMR in 21% (7 of 34) of cases. The diagnostic performance of QFR and FFR was similar but modest with MPS or CMR as reference. Comparable performance levels for QFR and FFR are encouraging for this pressure wire-free diagnostic method.