A system and a method for measuring impedance of a fuel cell stack are disclosed. The system includes: an energy consumption device, a cooling device, and a high-voltage battery connected in parallel to a main bus end of a fuel cell stack; a relay provided at the main bus end and configured to electrically connect or disconnect the cooling device and the high-voltage battery to or from the fuel cell stack; an impedance measurement unit configured to apply an AC current to the fuel cell stack and to measure the impedance of the fuel cell stack; and a controller configured to turn off the relay during measurement of the impedance of the fuel cell stack.