The COVID-19 pandemic put emergency departments all over the world under severe and unprecedented distress. Previous methods of evaluating patient flow impact, such as in-situ simulation, tabletop studies, etc., in a rapidly evolving pandemic are prohibitively impractical, time-consuming, costly, and inflexible. For instance, it is challenging to study the patient flow in the emergency department under different infection rates and get insights using in-situ simulation and tabletop studies. Despite circumventing many of these challenges, the simulation modeling approach and hybrid agent-based modeling stand underutilized. This study investigates the impact of increased patient infection rate on the emergency department patient flow by using a developed hybrid agent-based simulation model. This study reports findings on the patient infection rate in different emergency department patient flow configurations. This study’s results quantify and demonstrate that an increase in patient infection rate will lead to an incremental deterioration of the patient flow metrics average length of stay and crowding within the emergency department, especially if the waiting functions are introduced. Along with other findings, it is concluded that waiting functions, including the waiting zone, make the single average length of stay an ineffective measure as it creates a multinomial distribution of several tendencies.