The thermal management of a proton exchange membrane fuel cell (PEMFC) is crucial for fuel cell vehicles. This paper presents a new simulation model for the water-cooled PEMFC stacks for automotive vehicles and cooling systems. The cooling system model considers both the cooling of the stack and cooling of the compressed air through the intercooler. Theoretical analysis was carried out to calculate the heat dissipation requirements for the cooling system. The case study results show that more than 99.0% of heat dissipation requirement is for thermal management of the PEMFC stack; more than 98.5% of cooling water will be distributed to the stack cooling loop. It is also demonstrated that controlling cooling water flow rate and stack inlet cooling water temperature could effectively satisfy thermal management constraints. These thermal management constraints are differences in stack inlet and outlet cooling water temperature, stack temperature, fan power consumption, and pump power consumption.