A multiport bidirectional dc-dc converter with a diagnosis function for fuel cells that employs electrochemical impedance analysis was developed. The proposed converter, which is connected to electric double layer capacitors, can freely adjust the fuel cell voltage without fluctuation of the load voltage. A signal that consists of multiple frequency sinusoidal waves is superimposed as a duty ratio signal of the chopper circuit connected to the fuel cell, which enables simultaneous impedance measurement for these frequencies. The voltage and current values of the fuel cell are acquired by a digital signal processor to conduct fast Fourier transform calculations that give voltage and current spectra. The fraction of the spectra yields the electrochemical impedance. Experiments were conducted to validate the proposed method using a polymer electrolyte membrane fuel cell. The sinusoidal waves in the imposed signal have multiple frequencies to reduce the measuring time. The impedance characteristics determined using the proposed method are in good agreement with those obtained with an electrochemical instrument. To demonstrate the proposed method, the Nyquist plots when the fuel cell current, the operation temperature, and the stoichiometric ratios were changed and produced using the proposed method.