A system and method for putting a fuel cell vehicle system into a stand-by mode where there is little or no power being consumed, the quantity of fuel being used is minimal and the fuel cell system is able to quickly recover from the mode. The method includes determining whether predetermined stand-by mode vehicle level entrance criteria have been satisfied at a vehicle control level and predetermined stand-by mode fuel cell level entrance criteria have been satisfied for a fuel cell system control level, and putting the vehicle in the stand-by mode if both the vehicle level entrance criteria and the fuel cell level entrance criteria have been satisfied. The method exits the stand-by mode if predetermined vehicle level exit criteria have been satisfied or predetermined fuel cell level exit criteria have been satisfied.