A proton exchange membrane fuel cell (PEMFC) inevitably experiences performance degradation during long-term operation under various corrosive conditions. In particular, cell operation under cathode flooding conditions results in severe cell degradation through sequential processes that induce the degradation of each component in the membrane electrode assembly (MEA). Furthermore, an excessive amount of water remaining at the cathode can diffuse into the anode side (back diffusion of water), and repeated instances can cause anode flooding (leading to fuel starvation). Herein, we focus on the collateral anode degradation of a stationary PEMFC operating under cathode flooding conditions with an oversaturated cathode in terms of relative humidity (RH, 150% RH). We suggest low-humidity electrochemical impedance spectroscopy (EIS-RH30) as a fault identification method to detect the degradation of the MEA, including the anode, before severe cell deterioration. Specifically, the EIS-RH30 analysis enables the detection of the malfunctioning anode reaction by limiting the hydrogen oxidation reaction (HOR) and proton conductivity, through which the phase difference between transporting protons from the anode to the cathode can be reflected as the horizontal aspect of the Warburg impedance. A generalized finite-length Warburg is introduced to understand the variation in the Warburg impedance spectra, and its numerical analysis can act as a diagnosable signal to monitor the sequential degradation of an MEA. A feasibility study of EIS-RH30 on actual degradation behavior that occurs under cathode flooding conditions was performed along with a microstructural investigation inside the MEA.