In proton exchange membrane fuel cell (PEMFC) operations, the electrochemical reactions produce a rise in temperature. A fuel cell stack therefore requires an effective cooling system for optimum performance. In this study, miniature heat pipes were applied for cooling in PEMFC. Three alternatives were considered in tests: free convection, forced convection cooling with air, and also water. An analytical model was developed to show the possibility of evoking heat from inside a fuel cell stack with different numbers of miniature heat pipes. An experiment setup was designed and then used for further analysis. The proposed experiment setup consisted of a simulated fuel cell that produced heat and a number of thermosyphon miniature heat pipes to evoke heat from the simulated fuel cell. The experiment results reported in this paper present advantages and disadvantages of each tested cooling scenario. Results show that each cooling scenario, using a different number of heat pipes, provided different heat removal rates for PEMFC cooling.