This work develops an 8th order, non-linear thermal model of an automotive proton exchange membrane (PEM) fuel cell system. Subsystem models are developed from first principals where ever possible and validated against data from a physical system. The system model is validated against data from an automotive 120kW fuel cell system, with good agreement. Next, a reduced order model is constructed from the full model and the performance of the two models are compared. The reduced order linear model provided an acceptable representation of the full non-linear model.