A fuel cell voltage recovery system includes a fuel cell stack having a fuel cell stack voltage between fuel cell stack terminals which is at a first voltage during normal fuel cell operation. The system also includes a high voltage electrical system operating at a first DC operating voltage that is generally higher than the first voltage of the fuel cell stack. A boost converter in electrical connection with the fuel cell stack and the high voltage electrical system operates in a normal control mode to transfer electrical power from the fuel cell stack to the high voltage electrical system through regulation and control of average stack output current (boost input current) during normal fuel cell operation. The boost converter can also operate in a voltage control mode to lower the fuel cell stack voltage to a second voltage that is lower than the first voltage. A FCS controller controls the operation of the boost converter.