How emergency departments of different levels and types cope with a large-scale contagious infectious disease is unclear. We retrospectively analyzed the response of 100 emergency departments regarding use of personal protective equipment (PPE) and implementation of infection control measures (ICMs) during the severe acute respiratory syndrome outbreak in Taiwan. Emergency department workers in large hospitals were more severely affected by the epidemic. Large hospitals or public hospitals were more likely to use respirators. Small hospitals implemented more restrictive ICMs. Most emergency departments provided PPE (80%) and implemented ICMs (66%) at late stages of the outbreak. Instructions to use PPE or ICMs more frequently originated by emergency department administrators. The difficulty of implementing ICMs was significantly negatively correlated with their effectiveness. Because ability to prepare for and respond to emerging infectious diseases varies among hospitals, grouping infectious patients in a centralized location in an early stage of infection may reduce the extent of epidemics.