The PEFC stack in a commercial power system was operated with room air and pure hydrogen. After the system reached a steady temperature, an ac impedance test was conducted on the fuel cell power system. The impedance data were real-time response generated by the ac sinusoidal excitation. Data for a single PEM stack and PEM stacks operating in parallel and series were collected with or without an embedded system controller board and electronic devices. The equivalent circuit model with three time constants and the non-linear least square fitting program (NLLS) were applied for fitting the stack impedance spectrum. The Levenberg–Marquardt algorithm utilized in the NLLS fitting process automatically adjusted the parameter values of the physical elements in the model to find the best fit result. From the preliminary results, data interpretation and the equivalent circuit model identified the physical elements, the related electrochemical processes, and the phenomenon inside the fuel cells or stacks. Losses from ohmic conduction, anode activation, cathode activation, and mass transfer were separated and analyzed. Further PSpice simulation curves using these equivalent circuit elements demonstrate good agreement with the pulse testing data measured from the PEFC power system.