Recently, fractional flow reserve (FFR) derived from coronary computed tomography angiography (CCTA) (FFR_CT) has been developed. However, FFR_CT cannot be calculated for all patients from CCTA datasets. The purpose of the present study, therefore, was to evaluate the predictors that results in cases being inappropriate for FFR_CT processing. This study was a sub-analysis of the TRACT trial, from which 50 patients were divided into 2 groups according to FFR_CT measurability (measurable [group M] or not measurable [group N]) using CCTA examination at baseline. Thirty-nine (78%) patients comprised group M and 11 (22%) comprised group N. Heart rate at CCTA examination (72 beats/min vs. 63 beats/min; p = 0.007) and Agatston score (665 vs. 33; p = 0.002) in group N were significantly higher than those in group M. Multivariate logistic regression analyses revealed that heart rate at CCTA examination (OR 1.348 [95% CI 1.167–1.556]; p < 0.001) and Agatston score (OR 1.002 [95% CI 1.000–1.003]; p = 0.004) were significant, independent factors associated with non-measurability of FFR_CT. The frequency of poor image quality was highest in patients with heart rate > 65 beats/min and Agatston score > 400 (p < 0.0001). In conclusions, high heart rate at the time of CCTA examination and higher Agatston score were associated with poor image quality that resulted in cases being inappropriate for FFR_CT processing. Heart rate control at CCTA examination is necessary to acquire good-quality images required for computing FFR_CT.