The proton exchange membrane fuel cell (PEMFC) stands at the forefront of advancing energy sustainability. Effective monitoring, control, diagnosis, and prognosis are crucial for optimizing the PEMFC system’s sustainability, necessitating a dynamic model that can capture the transient response of the PEMFC. This paper uses a dynamic fractional-order model to describe the behaviors of a stationary micro combined heat and power (mCHP) PEMFC stack. Based on the fractional-order equivalent circuit model, the applied model accurately represents the electrochemical impedance spectroscopy (EIS) and the dynamic voltage response under transient conditions. The applied model is validated through experiments on an mCHP PEMFC stack under various fault conditions. The EIS data is analyzed under different current densities and various fault conditions, including the stoichiometry of the anode and cathode, the stack temperature, and the relative humidity. The dynamic voltage response of the applied model shows good correspondence with experimental results in both phase and amplitude, thereby affirming the method’s precision and solidifying its role as a reliable tool for enhancing the sustainability and operational efficiency of PEMFC systems.