A system and method for controlling the voltage on a high voltage bus in a fuel cell system in response to a failed high voltage battery. The method includes determining if the high voltage battery has failed, and disconnecting the battery from the high voltage bus in response to a failure. The method measures the voltage of the fuel cell stack by a DC boost circuit and converts the measured voltage to a voltage set-point value that sets the voltage on the high voltage bus, where the voltage set-point value changes as the measured voltage changes. A supervisory controller sets the media flow to the fuel cell stack and determines a minimum stack voltage limit value based on the stack maximum current draw that is used to determine a high voltage bus lower limit value.