Abstract The study indicates a comparison of PEM fuel cell systems (cathodic plate) with previous experimental setup and a new nano-design manufacturing for the nano-micro scale fluids with the fuel of hydrogen gas. The scope of the study is to demonstrate a superiority of fuel cell efficiency as well as genuine design over the experimental commercial fuel cell. Finding results of the energy efficiency was found to be 72.4% and exergy efficiency’s 85.22% of the PEMFC under 0.5 bar pressure and 0.2 l/min flow rate. Finding results revealed that the thermodynamic efficiency of PEMFC could be enhanced by regulating the pressure and flow rate parameters. This work gave great results thanks to the new design manufacturing. The results of this study emphasize to give better results compared to the results of the previous study. Besides supporting the previous study, it yielded even better results. Thus, it is thought that there will be a support energy system for larger energy systems in the future.