Real time analysis on impedance spectroscopy in PEFC (Polymer Electrolyte Fuel Cell) is tried using FFT (Fast Fourier Transform) method. It is proved this method can analyze the Cole·Cole plots of PEFC with high speed and high accuracy compared to conventional FRA (Frequency Response Analyzer). PEFC is simulated to equivalent circuit model with four resistances and three capacitances, and effects of running condition on those are analyzed by experiment. Results show this method has capability of on-board diagnosis and fuel cell system control.