Purpose: In order to improve the safety, capacity, economy, and sustainability of air transportation, revolutionary changes are required. These changes might range from the introduction of new technology and operational procedures to unprecedented roles of human operators and the way they interact. Implementing such changes can introduce both negative and positive emergent behaviour. i.e. behaviour that arises from the interactions between system entities as proposed in innovative concepts. Currently, the inability to understand and control such behaviour prevents us from avoiding undesired negative emergent behaviours and promoting positive ones. In order to address this problem, this thesis aims to understand emergent behaviour in the complex socio-technical air transportation system. Methods: The thesis proposes Agent-Based Modelling and Simulation (ABMS) as a method for capturing emergent behaviour of the socio-technical air transportation system, and evaluating novel system designs. The popularity of ABMS is driven by its capability of handling the increasing complexity of real world socio-technical systems that exhibit emergent behaviour. This thesis focuses on two main applications namely: 1) the identification of emergent safety risk of an active runway crossing operation; and 2) the evaluation of the role of coordination in Airline Operations Control (AOC) resilience. In both applications, ABMS has emerged as a key method because it is widely used in complexity science to understand how interactions give rise to emergent behavior. The agent-based models include all relevant human and technical agents, such as pilots and controllers and the decision support systems involved. Simulation of these agents interacting together is conducted to predict the impact of both existing and future concepts of operation. Results: The applications in this thesis highlight that ABMS has the capability to reveal unexpected emergent behaviour and provide novel insights in air transportation. For the airport safety application, various types of emergent behaviour have been revealed due to the development and simulation of the agent-based model that covers the totality of interactions of components and their variability in performance over time. The Monte Carlo simulations make it possible to understand the potential of agents in restricting the risk in off-nominal scenarios, through capturing their stochastic nature and accounting for uncertainty. For the airline resilience application, novel insights were gained about the role of coordination in airline resilience. Capitalizing on established airline practice and research about human coordination from the psychology domain, the agent-based simulations evaluated the operational effects of AOC coordination policies on a challenging disruption scenario. Conclusions & possible applications and implications: This thesis demonstrates that ABMS of air transport operations is a viable approach in gaining knowledge about emergent behaviour which was unknown before. This knowledge includes both bottlenecks of system designs and identified opportunities, and hence can be used to control and further optimize the socio-technical air transportation system. This also implies that ABMS can be a cost-effective method for evaluating new concepts during the early design phase of air transport operations.