A locomotive air brake control system that responds to penalty braking requests from external systems by applying a varying amount of train brake level based on monitored and calculated parameters in order to enforce a defined train condition. The system may include a minimum acceptable train braking, a condition to be achieved to prevent further application of train brakes, and a maximum train brake level to be applied in response to the request. Alternatively, the system may apply braking in stepped levels according defined thresholds for a train behavior variable of interest such as speed or deceleration. The system may be configured to incrementally apply and release train brakes during the adaptive penalty, and may also adjust the level of braking according to calculated braking capacity of the train.