Objective: Evidence supports the efficacy of coronary computed tomography angiography (CCTA)-based risk scores in cardiovascular risk stratification of patients with suspected coronary artery disease (CAD). We aimed to compare two CCTAbased risk score algorithms, Leiden and Confirm scores, in patients with diabetes mellitus (DM) and suspected CAD. Materials and Methods: This single-center prospective cohort study consecutively included 1241 DM patients (54.1% male, 60.2 ± 10.4 years) referred for CCTA for suspected CAD in 2015–2017. Leiden and Confirm scores were calculated and stratified as < 5 (reference), 5–20, and > 20 for Leiden and < 14.3 (reference), 14.3–19.5, and > 19.5 for Confirm. Major adverse cardiovascular events (MACE) were defined as the composite outcomes of cardiovascular death, nonfatal myocardial infarction (MI), stroke, and unstable angina requiring hospitalization. The Cox model and Kaplan–Meier method were used to evaluate the effect size of the risk scores on MACE. The area under the curve (AUC) at the median follow-up time was also compared between score algorithms. Results: During a median follow-up of 31 months (interquartile range, 27.6–37.3 months), 131 of MACE were recorded, including 17 cardiovascular deaths, 28 nonfatal MIs, 64 unstable anginas requiring hospitalization, and 22 strokes. An incremental incidence of MACE was observed in both Leiden and Confirm scores, with an increase in the scores (log-rank p < 0.001). In the multivariable analysis, compared with Leiden score < 5, the hazard ratios for Leiden scores of 5–20 and > 20 were 2.37 (95% confidence interval [CI]: 1.53–3.69; p < 0.001) and 4.39 (95% CI: 2.40–8.01; p < 0.001), respectively, while the Confirm score did not demonstrate a statistically significant association with the risk of MACE. The Leiden score showed a greater AUC of 0.840 compared to 0.777 for the Confirm score (p < 0.001). Conclusion CCTA-based risk score algorithms could be used as reliable cardiovascular risk predictors in patients with DM and suspected CAD, among which the Leiden score outperformed the Confirm score in predicting MACE.