Background: Cardiac screening using coronary computed tomography angiography (CCTA) in kidney transplant candidates before transplantation yields both diagnostic and prognostic information. Whether CT-derived fractional flow reserve (FFRCT) analysis provides prognostic information is unknown. This study aimed to assess the prognostic value of FFRCT for predicting major adverse cardiac events (MACE) and all-cause mortality in kidney transplant candidates. Methods: Among 553 consecutive kidney transplant candidates, 340 CCTA scans (61%) were evaluated with FFRCT analysis. Patients were categorized into groups based on lowest distal FFRCT; normal >0.80, intermediate 0.80–0.76, and low ≤0.75. In patients with ≥50% stenosis, a lesion-specific FFRCT was defined as; normal >0.80 and abnormal ≤0.80. The primary endpoint was MACE (cardiac death, resuscitated cardiac arrest, myocardial infarction or revascularization). The secondary endpoint was all-cause mortality. Results: Median follow-up was 3.3 years [2.0–5.1]. MACE occurred in 28 patients (8.2%), 29 patients (8.5%) died. When adjusting for risk factors and transplantation during follow-up, MACE occurred more frequently in patients with distal FFRCT ≤0.75 compared to patients with distal FFRCT >0.80: Hazard Ratio (HR): 3.8 (95%CI: 1.5–9.7), p < 0.01. In the lesion-specific analysis with <50% stenosis as reference, patients with lesion-specific FFRCT >0.80 had a HR for MACE of 1.5 (95%CI: 0.4–4.8), p = 0.55 while patients with lesion-specific FFRCT ≤0.80 had a HR of 6.0 (95%CI: 2.5–14.4), p < 0.01. Abnormal FFRCT values were not associated with increased mortality. Conclusion: In kidney transplant candidates, abnormal FFRCT values were associated with increased MACE but not mortality. Use of FFRCT may improve cardiac evaluation prior to transplantation.