Runway overruns (ROs) are the result of an aircraft rolling beyond the end of a runway, which is one of the accident’s types that most frequently occurs on aviation. The risk of an RO arises from the synergistic effect among its precursors, such as unstable approaches, long touchdowns and inadequate use of deceleration devices. To analyse this complex socio-technical system, the current work proposes a customised functional resonance analysis method, called FRAM-FDM, as traditional techniques of risk and safety assessment do not identify the interactions and couplings between the various functional aspects of the system itself, especially regarding human and organisational components. Basically, FRAM-FDM is the coupling of a traditional FRAM with flight data monitoring (FDM) techniques, used here to quantify the variabilities of the flight crew performance while executing the required activity (i.e. the landing). In this proposal, these variabilities (i.e. the FRAM functions aspects) are aggregated by the addend of a logistic regression, resulting in a model to evaluate the flare operations and the brake application profile effect on the remaining distance to the end of the runway, used as a reference to classify the landing as acceptable or not. The present application of the FRAM-FDM assesses the operational risk of a sample fleet in overrunning the runway during landing, highlighting the brake pedal application profile as the most relevant contributor. The model improves the knowledge about the system behaviour, being useful to direct flight crew training.