Airports worldwide have undergone a significant transformation to provide a more efficient, secure, and enjoyable travel experience for passengers. The delays or inefficiency of aviation security checks not only reduces the effectiveness of airport security operations, but also leads to worthening of passengers’ experience and increases criminal and terrorist threats. This paper examines the issue of airport security system modelling with AnyLogic simulation to increase its efficiency, using Dublin Airport as a case study. The research aimed to identify the causes of queues in the airport security lanes and to develop recommendations for airport authority regarding optimal resources utilization at the security checkpoints. Various airport security systems were analyzed in the paper, followed with the airport’s epidemiological safety assessment through the correspondent optimization experiments in the simulation software AnyLogic. The research results indicate the necessity to implement a new strategy for improving the efficiency of the airport security procedures. It was found that the optimal security system for the case airport is Rapiscan 620XR. It can reduce the average passenger’s processing time at security checkpoint to 0.635 min. It was also determined that in case of the new security system usage the morning hours (6 am–1 pm) are the least congested with the resources utilization at 78%, while the system operates at full capacity during the afternoon and evening hours. In future research, it would be beneficial to evaluate alternative simulation tools and examine other scenarios to compare their outcomes with the results discussed in this paper.