The adequate water content is one of essential factors affecting the performance of PEMFCs using the perfluorosulfonic acid membrane. An external humidifier is generally used for water supply, but the increase in mass and volume degrades the total system efficiency. In this study, the performance of a self-humidifying PEMFC was analyzed with two different membranes. The optimal operating conditions were obtained by using the response surface methodology. For the high voltage region, the performance of the PEMFC with Aquivion increased with the increase in operating temperature unlike that with Nafion due to their difference of water retention. For the low voltage region, the similar performance variation was observed for both membranes.