A stack in the proton exchange membrane fuel cell (PEMFC) consists of bipolar plates, a membrane electrode assembly, a gas diffusion layer, a collector and end plates. High current density is usually obtainable partially from uniform temperature distribution in the fuel cell. A size optimization method considering the thermal expansion effect of stacked plates was developed on the basis of finite element analyses. The thermal stresses in end, bipolar, and cooling plates were calculated based on temperature distribution obtained from thermal analyses. Finally, the optimization method was applied and optimum thicknesses of the three plates were calculated considering both fastening bolt tension and thermal expansion of each unit cell (72 cells, 5kW). The optimum design considering both thermal and mechanical loads increases the thickness of an end plate by 0.64-0.83% the case considering only mechanical load. The effect can be enlarged if the number of stack increases as in an automotive application to 200-300 stacks.