Purpose Commercial aviation is feasible thanks to the complex socio-technical air transportation system, which involves interactions between human operators, technical systems, and procedures. In view of the expected growth in commercial aviation, significant changes in this socio-technical system are in development both in the USA and Europe. Such a complex socio-technical system may generate various types of emergent behavior, which may range from simple emergence, through weak emergence, up to strong emergence. The purpose of this paper is to demonstrate that agent-based modeling and simulation allows identifying changed and novel rare emergent behavior in this complex socio-technical system. Methods An agent based model of a specific operation at an airport has been developed. The specific operation considered is the controlled crossing by a taxiing aircraft of a runway that is in use for controlled departures. The agent-based model includes all relevant human and technical agents, such as the aircraft, the pilots, the controllers and the decision support systems involved. This agent-based model is used to conduct rare event Monte Carlo (MC) simulations. Results The MC simulation results obtained confirm that agent based modeling and simulation of a socio-technical air transportation system allows to identify rare emergent behavior that was not identified through earlier, non-agent-based simulations, including human-in-the-loop simulations of the same operation. A typical example of such emergent behavior is the finding that alerting systems do not really reduce the safety risk. Conclusions Agent based MC simulations of commercial aviation operations has been demonstrated as a viable way to be evaluated regarding rare emergent behaviour. This rare emergent behaviour could not have been found through the more traditional simulation approaches.