Proton exchange membrane fuel cell, which utilizes mainly hydrogen for fuel, has many advantages for vehicle applications. Compared to conventional low-temperature proton exchange membrane fuel cell (60–80 °C), high-temperature fuel cell (120–180 °C) requires a simpler system. It is characterized by enhanced electrochemical kinetics and can use liquid fuel such as methanol due to higher carbon monoxide tolerance. In this paper, phosphoric acid doped high-temperature proton exchange membrane fuel cell with a reformer system is applied for powering an automotive vehicle. Thermal management and control of the fuel cell stack for performance optimization remain critical. This paper aims to analyze the heat dissipation requirement for high-temperature fuel cell vehicles and propose cooling strategies for optimizing the performance. A simulation model of the high-temperature proton exchange membrane fuel cell stack and its oil cooling system were developed. The stack model had been validated against experimental results. The case study results show that increasing carbon monoxide concentration will increase the voltage loss. Increased operating temperature to 448 K reduces the stack heat generation due to the poisoning effect. It is suggested to keep the inlet cooling oil temperature constant within the range of 435–445 K and adjust the cooling oil flow rate (2.5–5 kg/s) to meet the heat dissipation requirement for the fuel cell stack. Due to the significant temperature difference between the fuel cell and the external environment (>150 K), the recoverable waste heat is about 39 kW.