The diagnostic accuracy of non-invasive diagnostic methods for detecting coronary artery disease has increased in recent years. This study aimed to assess the diagnostic performance of ¹⁵O-water positron emission tomography (PET) in terms of stress myocardial blood flow (MBF) and myocardial flow reserve (MFR) in patients with single-vessel disease referred for percutaneous coronary intervention (PCI), using fractional flow reserve (FFR) value of ≤0.80 as the reference for a significant stenosis. We also assessed the influence of the index of microcirculatory resistance (IMR) on the diagnostic performance of PET. ¹⁵O-water PET FFR and IMR were measured before PCI in 26 patients with single-vessel disease. Stress MBF < 2.5 ml/min/g (95% confidence interval [CI]) had sensitivity 78% (95% CI: 52%–94%), specificity 50% (95% CI: 16%–84%), positive predictive value (PPV) 78% (95% CI: 63%–88%), negative predictive value (NPV) 50% (95% CI: 25%–75%), and accuracy 69% (95% CI: 48%–86%). MFR < 2.5 had sensitivity 72% (95% CI: 47%–90%), specificity 75% (95% CI: 35%–97%), PPV 87% (95% CI: 65%–96%), NPV 55% (95% CI: 34%–74%), and accuracy 73% (95% CI: 52%–88%). In patients with IMR > 24, stress MBF correlated with FFR (r = 0.651; p = 0.016) whereas stress MBF did not correlate with FFR in patients with IMR < 24. In conclusion, stress MBF and MFR had modest diagnostic performance compared to invasive FFR measurements in patients with single-vessel disease.