An emergency power supply system for a fuel cell-powered vehicle is provided. In particular, the system includes a low voltage DC-DC converter (LDC) designed to convert an output voltage from either a fuel cell stack, or a bi-directional high voltage DC-DC converter into a low voltage and supply the low voltage to a low voltage battery, a DC-DC converter designed to convert an output voltage from either the fuel cell stack or the bi-directional high voltage DC-DC converter into a low voltage, and a fuel cell controller designed to determine whether to supply an output voltage from the DC-DC converter to an output voltage supply line of the low voltage battery.