A great challenge for cognitive neuroscience is studying human behavior in its complexity as it manifests in the real world. The field of aviation provides a unique opportunity to investigate how perception, action and cognition interact in complex yet controlled ecologically valid environments. We suggest a novel cross-domain approach that combines insights from ecological psychology and embodied cognition with a neurophysiological framework to explain patterns of human performance across a variety of aviation contexts. Specifically, we argue that studying the interaction between an agent and the environment, as manifest in the Mirror Neuron system as a neural correlate, is key to understanding complex behavior. We can describe the experience and skills involved with task-relevant actions—like flying an airplane—using brain mechanisms of motor simulation of the observed action. With this direct coupling between perception and action, the automatic implicit nature of the Mirror Neuron system can be harnessed to improve human factor and ergonomics. This analysis offers three areas for future study and application: (1) enhancing flight training by isolating specific agent-environment relations; (2) tracking training progression based on brain signatures of flight expertise; and (3) neuroscientific-inspired ecological design of next-generation human–machine interfaces in flight decks.