Background. Waiting times for access to care, for example, for diagnostic imaging or surgery, are a highly relevant issue in health care. Waiting or deferred treatment caused by limited resource capacities can affect treatment success, quality of life, and costs. However, when treatment alternatives are compared in economic models, often unrestricted availability of resources is assumed, and dynamic changes in waiting lines remain unconsidered. The objective of this study was to evaluate the impact of potential real-world capacity restrictions and implied waiting lines on cost-effectiveness results and additional model outcomes. Methods. A case study of drug-eluting and bare-metal stent treatment illustrates the effect of hypothetical capacity limitations of daily stenting procedures. Therefore, a decision-analytic model which allows for explicitly defined resource capacities and dynamic waiting lines was built using discrete event simulation. Cost-effectiveness, utilization, waiting time, and budgetary impact of alternative treatment scenarios are analyzed under the assumption of limited and unlimited resource capacities. Results. The compared treatment allocation scenarios in the case study demonstrate that the additional cost for waiting increases the average treatment cost per patient. The different scenarios have different impacts on waiting lines because of the number of repeated interventions. Additionally, this effect leads to changes in cost-effectiveness results for the hypothetical capacity limit. Explicitly modeled capacities allow for further analysis of capacity utilization, waiting lines, and budgetary impact. Conclusion. Our model shows that neglected limited capacities can cause wrong cost-effectiveness results. Therefore, capacities should be explicitly included in decision-analytic models if there is evidence of scarcity.