Higher energy densities and the potential for nearly instantaneous recharging make microscale fuel cells very attractive as power sources for portable technology in comparison with standard battery technology. Heat management is very important to the microscale fuel cells because of the generation of waste heat. Waste heat generated in polymer electrolyte membrane fuel cells includes oxygen reduction reaction in the cathode catalyst, hydrogen oxidation reaction in the anode catalyst, and Ohmic heating in the membrane. A novel microscale fuel cell design is presented here that utilizes a half-membrane electrode assembly. An ANSYS Fluent model is presented to investigate the effects of operating conditions on the heat management of this microscale fuel cell. Five inlet fuel temperatures are 22°C, 40°C, 50°C, 60°C, and 70°C. Two fuel flow rate are 0.3 mL/min and 2 mL/min. The fuel cell is simulated under natural convection and forced convection. The simulations predict thermal profiles throughout this microscale fuel cell design. The exit temperature of fuel stream, oxygen stream and nitrogen stream are obtained to determine the rate of heat removal. Simulation results show that the fuel stream dominates heat removal at room temperature. As inlet fuel temperature increases, the majority of heat removal occurs via convection with the ambient air by the exposed current collector surfaces. The top and bottom current collector removes almost the same amount of heat. The model also shows that the heat transfer through the oxygen channel and nitrogen channel is minimal over the range of inlet fuel temperatures. Increasing fuel flow rate and ambient air flow both increase the heat removal by the exposed current collector surfaces. Ultimately, these simulations can be used to determine design points for best performance and durability in a single-channel microscale fuel cell.