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The on‐road monitoring of polymer electrolyte membrane fuel cells (PEMFCs) in automotive systems optimizes their efficiency and fuel consumption in addition to increasing their lifetime. In this work, electrochemical impedance spectroscopy (EIS) measurements and special EIS data analysis algorithms were used to quickly identify fuel cell operational modes and failures during cell operation. The approach developed enables the measurement and analysis time of only a few seconds and allows the accurate extraction of information about the membrane and charge transfer resistance. The data analysis procedures show similar accuracy to that of the complex non‐linear least square fitting algorithms. As a result, typical operational failures like air and hydrogen starvation were able to be easily distinguished, and different operational states (membrane humidification, air stoichiometry) of the PEMFCs could be identified.