Efficient team decision making has become vital in organizations, dominated by the complex system of systems (SoS). Inefficient decisions can result in significant extra cost and reduction in the overall performance within the organizations. Therefore, SoS success requires an adaptable design that can proactively evaluate and modify decisions in a dynamic process. Improved systems engineering (SE) processes and tools are needed during the systems’ development lifecycle to make decisions, and rapidly evaluate and assess multiple design alternatives to effectively select the architectural design strategies that yield the highest mission performance. This research aims to increase the knowledge of SoS engineering by developing an agent-based model of team collaboration in an operational SoS. The model evaluates and selects the decision(s) for SoS comprised of collaborative teams that result in higher mission performance. The proposed agent-based model was applied to test the team decision-making improvements within the SoS structure of the air transportation domain. The experimental results indicated significant improvements in decision coordination, decision workload, and overall mission performance in the air transportation domain. This research contributes to the agent-based modeling of the SoS teams and can assist with evaluating team decisions and improving decision making as an essential element in the field of SE.