The resting full-cycle ratio (RFR), a novel resting index, is well correlated with and shows good diagnostic accuracy to the fractional flow reserve (FFR). However, discordance results between the RFR and FFR have been observed to occur in about 20% of cases. This study aimed to clarify the prevalence and factors of discordant results between the RFR and FFR through a direct comparison of these values in daily clinical practice. A total of 220 intermediate coronary lesions of 156 consecutive patients with RFR and FFR measurements were allocated to four groups according to RFR and FFR cutoff values. We compared the angiographic, clinical, and hemodynamic variables among the groups. Discordant results between the RFR and FFR were observed in 19.6% of vessels, and the proportion of discordant results was significantly higher in the left main trunk and left anterior descending artery (LM + LAD) than in non-LAD vessels (25.2% vs. 12.3%, p = 0.006). In the multivariable regression analysis, LM + LAD location, hemodialysis, and peripheral artery disease were associated with a low RFR among patients with a high FFR. Conversely, the absence of diabetes mellitus and the presence of higher hemoglobin levels were associated with a higher RFR among patients with a low FFR. Specific angiographic and clinical characteristics such as LM + LAD location, hemodialysis, peripheral artery disease, and absence of diabetes mellitus and anemia can be independent predictors of physiologic discordance between the RFR and FFR.