System and method for controlling operation of a vehicle in real-time with a supervisory control module. A fault detection module is configured to receive respective sensor data from one or more sensors in communication with the vehicle and generate fault data. The supervisory control module includes at least one fault-tolerant controller configured to respond to a plurality of faults. The supervisory control module is configured to receive the fault data. When at least one fault is detected from the plurality of faults, the supervisory control module is configured to employ the fault-tolerant controller to generate at least one selected command. The selected command is transmitted to one or more device controllers for delivery to at least one of the respective components of the vehicle. Operation of the vehicle is controlled based in part on the selected command.