The research works to reduce the capital and operating cost of the polymer electrolyte membrane fuel cell (PEMFC) have been performed since the cost competition is very important for the successful commercialization of the PEMFC system. In this paper, the cost optimal design to minimize the total cost of the PEMFC system has been proposed. In terms of the system design, the operating voltage of the unit cell is the key factor to decide the system efficiency and the capital cost. The number of the cells of the stack depends on the design value of the PEMFC cell voltage and vice versa. The operating cell voltage and the stack size determine the cost manufacturing the stack and the required amount of the cathodic and anodic fuel. In addition, the size and cost of its balance of plants (BOPs) are also changeable according to the amount of the both fuel. Thus it is noted that the cell voltage is the main design variable to minimize the capital and operating cost of the PEMFC. The proposed cost optimal design is based on the simulator including the efficiency models as well as the cost data for the stack and major BOPs. Furthermore, the proposed design method can be applied for the other application such as the automotive and portable fuel cell systems.