This study aims to apply lean thinking to the Emergency Department of Kocaeli University Education and Research Hospital. From analyzing to designing the improved system, lean techniques are adopted in order to reduce waste compared to the current system and to make the process continuous. Although lean defines wastes in the process, it does not indicate which wastes should be eliminated primarily. At this point, Arena simulation software program is used. To compare the current and simulated systems, the length of stay of patients in the Emergency Department is selected as the main quality measurement. According to Arena outcomes, the main bottlenecks are identified and then suggested improvements are implemented in the newly designed system with lean approaches. To determine the effects of the improvement, Arena is run again to see whether or not there is a significant difference. Taking into account these considerations, the Arena simulation program helped the application of lean tools in redesigning the Emergency Department process.