Abstract Background Incorporation of CT-derived fractional flow reserve (CT-FFR) enhances the precision of Coronary CT Angiography (CCTA) to detect hemodynamically significant coronary artery disease (CAD). However, the financial consequences remain unclear. Purpose Our objective is to assess the economic implications of CT-FFR in the Dutch Healthcare system. Methods This retrospective, single-center cost effectiveness analysis includes patient data of a previously published study assessing the impact of routine CT-FFR availability on clinical management. We collected medical resource use for both diagnostic and therapeutic cardiovascular care with a follow-up duration of 1 year. Costs of CT-FFR analysis were set at €1000, its current price for Dutch hospitals. Median total costs at were compared using the Wilcoxon rank sum test, including a sensitivity analysis in which cost estimations (without registered maximum tariffs) were increased or decreased with 10%. Results A total of 360 patients, classified as having low to intermediate risk of CAD, were enrolled in the study – 224 in the CCTA group and 136 in the CT-FFR group. In addition to undergoing more (invasive) diagnostic testing and revascularization procedures over the studied period, patients in the CCTA-group had more outpatient clinic consultations (p<0.001), presented more frequently to the emergency department (p=0.035) and spend more nights in the hospital (p=0.11). Median costs were €3.347 (IQR €1.066 – €4.862) in the CCTA-group and €1.436 (IQR €1.362 - €3.943) in the CT-FFR group (p=0.091). Increasing cost estimation with 10% revealed a median of €3.431 in the CCTA-group versus €1.479 in the CT-FFR group (p=0.078), decreasing with 10% showed median costs of €3.263 in the CCTA-group and €1.392 in the CT-FFR group (p=0.118). In our sample, CT-FFR guided care would have been significantly cheaper than CCTA-guided care at or below a market price of €770. Conclusion Despite the significant reduction in additional diagnostic testing and hospital visits in the CT-FFR group, CT-FFR guided care was not cheaper than CCTA-guided care at its current market price of €1.000. Economic cost-effectiveness would have occurred from a price of €770 per analysis. The large difference between medians suggests that the lack of significance might partially be attributed to insufficient power in this relatively small sample size. Additionally, this study did not account for costs associated with loss of productivity and quality of life. However, less additional diagnostic testing, less revascularization procedures and less hospital consultations and admissions leads to reduction in hospital resource consumption and patient burden, which is an important advantage of CT-FFR as the number of referred patients increases yearly.