The validity of electrochemical impedance measurements of polymer electrolyte fuel cells (PEFCs) have to be evaluated before an attempt is made to interpret the electrochemical mechanisms represented in the Nyquist plot. This evaluation can be carried out by data transformation of impedance measurements using Kramers-Kronig (K-K) relations. However, this evaluation has been commonly neglected in the fuel cell area due to the complexity of applying the mathematical K-K relations to real-world impedance measurements. In this study a computational algorithm, based on the Fast Fourier Transform (FFT) theory, the Hilbert transformation of impedance data, and a validated impedance model for PEFCs, for evaluating data transformation (real to imaginary Z’→Z’’ and imaginary to real Z’’→Z’) and hence validity of impedance measurements of PEFCs has been developed in Matlab®. With this computational algorithm it is possible to identify the factors that lead to incorrect EIS measurements of PEFCs such as inductance effect from the electrical cables of the measurement system, incorrect AC amplitude signal, and instability during EIS measurements. The computational algorithm developed in this study enables more accurate impedance results to be obtained to study the performance and state of health of PEFCs.