Disclosed herein is a method for diagnosing a fault of a fuel cell stack, the method including: applying a summed current obtained by summing first and second frequencies to the fuel cell stack; diagnosing whether or not a fault has been generated in the fuel cell stack using a higher frequency of first and second frequencies of output voltages of the fuel cell stack; and reconfirming whether or not the fault has been generated in the fuel cell stack using the first and second frequencies in the output voltage of the fuel cell stack.