The worldwide COVID-19 pandemic has had a tremendous impact on the aviation industry, with a reduction in passenger demand never seen before. To minimize the spread of the virus and to gain trust from the public in the airport operations’ safety, airports implemented measures, e.g., physical distancing, entry/exit temperature screening and more. However, airports do not know what the impact of these measures will be on the operations’ performance and the passengers’ safety when passenger demand increases back. The goal of this research is twofold. Firstly, to analyze the impact of current (COVID-19) and future pandemic-related measures on airport terminal operations. Secondly, to identify plans that airport management agents can take to control passengers’ flow in a safe, efficient, secure and resilient way. To model and simulate airport operations, an agent-based model was developed. The proposed model covers the main airport’s handling processes and simulates local interactions, such as physical distancing between passengers. The obtained results show that COVID-19 measures can significantly affect the passenger throughput of the handling processes and the average time passengers are in contact with each other. For instance, a 20% increase in check-in time (due to additional COVID-19 related paperwork at the check-in desk) can decrease passenger throughput by 16% and increase the time that passengers are in contact by 23%.