A fault clearing system and method for an engine control system includes a plurality of processor modules to control and monitor the engine and set a plurality of faults. The plurality of processor modules includes an electronic throttle control (ETC) module to control and monitor a throttle of the engine, and a plurality of engine sensors and ETC sensors. An ETC diagnostic module monitors the ETC sensors and engine sensors, with the ETC diagnostic module setting a low voltage induced fault. The ETC diagnostic module will also enter one of a plurality of low voltage states in response to the low voltage induced fault. The ETC diagnostic module selectively controls the ETC module and selectively clears the faults in the ETC module and plurality of processor modules upon entry into one of the low voltage states.