Polymer electrolyte membrane fuel cells (PEMFC) can be a promising energy source if optimal thermal management is provided, and also manufacturing cost is reduced for mass production. These are the main goals researchers have been recently pursuing to commercialize the PEMFCs. Here, a new simulation based design is proposed for a PEMFC with metallic bipolar plates. Using metal plates facilitates the manufacturing process and provides the possibility of forming them into desired shapes. Metallic bipolar plates are considered for both the reacting and cooling sites by pressing them into desired forms. Here, three different spacer plates as models A, B and C are designed to let fluid pass through the extruded site. The bipolar plate surface-averaged temperature is the parameter for evaluating the performance of the spacers in cooling strategy. Model C showing the best performance with least surface-averaged temperature among others, it was considered for further investigations. Moreover, spacer C is improved by punching some holes in critical regions to allow the fluid flow more easily in order to attain a uniform temperature distribution in lower Reynolds number. Using water based nanofluid with a concentration 5 vol%, the desired cooling performance is achieved at Reynolds number 500, which is reduced to a half if compared with the base fluid. Also, the innovative cooling design employed in our study is believed to exquisitely contract the size of a PEMFC and hence successfully reduce its weight.