In spite of valuable studies done so far on the field polymer electrolyte membrane fuel cells, one substantial question has not been answered yet; optimization considering which combination of performance criteria brings the greatest benefits. Here, to address and uncover the issue, an approach is proposed and implemented for a polymer electrolyte membrane fuel cell as the case study. Different optimization scenarios, in each of which one possible combination of efficiency, power density, levelized cost, and size is considered as the objective functions, are defined and having obtained and compared optimized answers of different scenarios, the best of them is selected based on the four mentioned preference criteria for transportation and stationary applications. In addition, impacts of variation of capacity on the results of decision making and corresponding values of the four performance criteria are investigated. The results show that optimizations considering power density and levelized cost are equivalent. Moreover, despite what may seem at first, multi-objective optimization considering all performance criteria as the objective functions is not the best solution, and for both applications and all studied capacities range from 10 to 100 kW, multi-objective optimization based on either power density or levelized cost and size is taken into account as the best optimization strategy.