A simulation and decision support system, RealOpt©, for planning large-scale emergency dispensing clinics to respond to biological threats and infectious disease outbreaks is described. The system allows public health administrators to investigate clinic design and staffing scenarios quickly. RealOpt© incorporates efficient optimization technology seamlessly interfaced with a simulation module. The system's correctness and computational advantage are validated via comparisons against simulation runs of the same model developed on a commercial system. Simulation studies to explore facility layout and staffing scenarios for smallpox vaccination and for an actual anthrax-treatment dispensing exercise and post event analysis are presented. The system produces results consistent with the model built on the commercial system, but requires only a fraction of the computational time. Each smallpox scenario runs within 1 CPU minute on RealOpt©, versus run times of over 5–10 h on the commercial system. The system's fast computational time enables its use in large-scale studies, in particular an anthrax response planning exercise involving a county with 864,000 households. The computational effort required for this exercise was roughly 30 min for all scenarios considered, demonstrating that RealOpt© offers a very promising avenue for pursuing a comprehensive investigation involving a more diverse set of scenarios, and justifying work towards development of a robust system that can be widely deployed for use by state, local, and tribal health practitioners. Using our staff allocation and assignments for the Anthrax field exercise, DeKalb county achieved the highest throughput among all counties that simultaneously conducted the same scale of Anthrax exercise at various locations, with labor usage at or below the other counties. Indeed, DeKalb exceeded the targeted number of households, and it processed 50% more individuals compared to the second place county. None of the other counties achieved the targeted number of households. The external evaluators commented that DeKalb produced the most efficient floor plan (with no path crossing), the most cost-effective dispensing (lowest labor/throughput value), and the smoothest operations (shortest average wait time, average queue length, equalized utilization rate). The study proves that even without historical data, using our system one can plan ahead and be able to wisely estimate the required labor resources. The exercise also revealed many areas that need attention during the operations planning and design of dispensing centers. The type of disaster being confronted (e.g., biological attack, infectious disease outbreak, or a natural disaster) also dictates different design considerations with respect to the dispensing clinic, facility locations, dispensing and backup strategies, and level of security protection. Depending on the situation, backup plans will be different, and the level of security and military personnel, as well as the number of healthcare workers required, will vary. In summary, the study shows that a real-time decision support system is viable through careful design of a stand-alone simulator coupled with powerful tailor-designed optimization solvers. The flexibility of performing empirical tests quickly means the system is amenable for use in training and preparation, and for strategic planning before and during an emergency situation. The system facilitates analysis of “what-if'' scenarios, and serves as an invaluable tool for operational planning and dynamic on-the-fly reconfigurations of large-scale emergency dispensing clinics. It also allows for “virtual field exercises” to be performed on the decision support system, offering insight into operations flow and bottlenecks when mass dispensing is required for a region with a large population. The system, designed in modular form with a flexible implementation, enables future expansion and modification regarding emergency center design with respect to treatment for different biological threats or disease outbreaks. Working with emergency response departments, further fine-tuning and development of the system will be made to address different biological attacks and infectious disease outbreaks, and to ensure its practicality and usability.