In this paper, an accurate model of proton exchange membrane fuel cell (PEMFC) for optimal identification of PEMFC parameters has been developed. The optimization methodology is based on the modified version of Manta Ray Foraging Optimization (MMRFO) technique for minimizing the sum of squared errors (SSE) between the Experimentally measured stack voltage and the estimated voltage produced by the optimized model. In the modified methodology, the sine-cosine method has been utilized to enhance the global searching capability in the exploration phase and the local searching capability in the exploitation phase of the MRFO algorithm. In order to validate the effectiveness of the suggested methodology, four different case studies comprising standard benchmark 250 W PEMFC, BCS-500 W PEMFC, SR-12 500 W FC, and 1 kW Temasek stacks were utilized, and the attainments have been compared with the measured polarization characteristics. The attainments have been intensively compared with several metaheuristic algorithms (MA) including Tree growth Algorithm (TGA), Grey wolf optimizer (GWO), Whale optimization algorithm (WOA), Salp swarm algorithm (SSA), and original Manta Ray Foraging Optimization (MRFO), to confirm the superiority of the MMRFO against the compared techniques. The obtained results give a satisfactory agreement between the MMRFO-based model and the experimentally measured data. Finally, the achievements confirmed the effectiveness of the MMRFO over the basic MRFO algorithm and other novel metaheuristic algorithms in identifying PEMFC parameters.