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With the increasing demand for electrical energy and the challenges related to its production, along with the need to be environmentally friendly to achieve sustainability for future generations, proton exchange membrane fuel cells (PEMFCs) are emerging as a clean energy source that can effectively replace conventional energy sources, in various fields of application and especially in the field of transportation exploiting electric vehicles (EVs). To improve the development and control of the PEMFCs, the precise determination of its mathematical model remains an essential task. Indeed, the accuracy of such a model depends on the ability to overcome the constraints associated with the nonlinearity and the numerous involved unknown parameters. The present paper proposes a new Dandelion Optimizer (DO) to accurately identify, for the first time, the parameters of the PEMFC model. The DO addresses the weaknesses of the majority of metaheuristic algorithms related to the self-adaptation of parameters, the stagnation of convergence to local minima, and the ability to refer to the whole population. The high ability of the proposed method is investigated using both steady-state and dynamic situations. The DO-based parameters estimation approach has been assessed through a specific comparative study with the most recently published techniques including GWO, GBO, HHO, IAEO, VSDE, and ABCDESC is performed using two typical PEMFC modules, namely 250 W PEMFC and NedStack PS6. The results obtained proved that the proposed approach obtained promising achievements and better performances comparatively with well-recognized and competitive methods.