Background and study aims: The projected increased demand for health services obligates healthcare organizations to operate efficiently. Discrete event simulation (DES) is a modeling method that allows for optimization of systems through virtual testing of different configurations before implementation. The objective of this study was to identify strategies to improve the daily efficiencies of an endoscopy center with the use of DES. Methods: We built a DES model of a five procedure room endoscopy unit at a tertiary-care university medical center. After validating the baseline model, we tested alternate configurations to run the endoscopy suite and evaluated outcomes associated with each change. The main outcome measures included adequate number of preparation and recovery rooms, blocked inflow, delay times, blocked outflows, and patient cycle time. Results: Based on a sensitivity analysis, the adequate number of preparation rooms is eight and recovery rooms is nine for a five procedure room unit (total 3.4 preparation and recovery rooms per procedure room). Simple changes to procedure scheduling and patient arrival times led to a modest improvement in efficiency. Increasing the preparation/recovery rooms based on the sensitivity analysis led to significant improvements in efficiency. Conclusions: By applying tools such as DES, we can model changes in an environment with complex interactions and find ways to improve the medical care we provide. DES is applicable to any endoscopy unit and would be particularly valuable to those who are trying to improve on the efficiency of care and patient experience.