Among the various types of fuel cells, the polymer electrolyte fuel cell (PEFC) is one of the prospective power sources for automotive applications, stationary cogeneration systems, and mobile electronic devices. The PEFC is very sensitive to the high temperature environment inside the fuel cell, and non-uniform temperature distribution reduces its performance. In this study, the performance of cooling plates for the PEFC was investigated by using three-dimensional computational fluid dynamics with commercial software. Six cooling plates were designed with different channel configurations. Models 1 and 4 had typical serpentine and parallel configurations, respectively. Models 2 and 3 had modified serpentine structures from Model 1, while Models 5 and 6 had modified parallel structures from Model 4. Models 1 and 2 showed relatively high temperatures around the outlet and the inlet area of the channel, respectively. Cooling performance of Models 4 and 5 was lower than that of Model 6 due to non-uniform fluid flow and temperature distributions. Models 3 and 6 showed higher cooling performance than serpentine type models and parallel type models, respectively. The performance of Model 3 was superior to that of Model 6 with respect to the control of the maximum surface temperature and uniformity. The thermal performance of Model 3 improved over Model 6 with the increase of heat flux. However, the pressure drop of Model 3 was higher than that of Model 6 because Model 3 had relatively high flow velocity through its channel and greater number of bends than Model 6.