In this research, a simulation based optimization strategy is developed to improve the operation of airport security screening checkpoints (SSCPs). The simulation based optimization strategy aims to improve any airport's SSCP operations by providing a flexible modeling approach to decide optimal checkpoint configurations and their corresponding workforce allocations. Simulation based optimization is a suitable technique for problems involving data uncertainties that evolve over time, requiring important system decisions to be made prior to observing the entire data stream. This is indeed the case in SSCPs, where the passenger arrival times are difficult to predict and requirements for equipment and human resources must be scheduled in advance. The team explicitly included the uncertainties associated with future passenger arrivals and availability and performance levels of the resources in computing staffing and system configuration decisions. The proposed simulation based optimization strategy provided a 31.4% improvement for the passengers' cycle time when compared to a benchmark scenario.