Disclosed herein is a method for diagnosing a fault of a fuel cell stack, including: applying a summed current obtained by summing currents of different frequency regions to the fuel cell stack; passing output voltages of the fuel cell stack through each of the different frequency filters to extract the respective diagnosis data; and diagnosing whether or not a fault has been generated in the fuel cell stack using the respective diagnosis data. Therefore, it is possible to further improve diagnosis analysis capability by applying the summed current obtained by summing the currents of the different frequency regions to the fuel cell stack and then rapidly diagnosing the fault of the fuel cell stack using the diagnosis data obtained by filtering the output voltages of the fuel cell stack.