To diagnose a fault of a fuel cell stack, an alternating current having a first optimal frequency of a first frequency domain to diagnose a drop in cell voltage and an alternating current having a second optimal frequency of a second frequency domain to diagnose a cause of the drop in cell voltage are supplied to the fuel cell stack are provided. A distortion rate is then calculated based on voltage of the fuel cell stack according to the alternating current of the first optimal frequency, and the drop in cell voltage is diagnosed based on the calculated distortion rate. Also, impedance is calculated based on voltage and a current of the fuel cell stack according to the alternating current of the second optimal frequency and amount of water is calculated based on the calculated in the fuel cell stack, and the cause of the drop in cell voltage is diagnosed based on the calculated impedance and amount of water.