Temperature changes in PEM fuel cell stacks affect gas transfer, water balance, and electrochemical reaction activities. Improper temperature regulation could impact the durability of the stack, which is of the highest importance for a city bus. Hence, thermal management is an important issue for PEM fuel cell, especially for city bus applications. In this study, a model-based control strategy aimed at keeping the temperature in a small range near target value was applied to a cooling system. Firstly, the cooling system of the PEM fuel cell system was proposed and the cause of temperature fluctuation was analyzed. Then, a model of the cooling system, which consisted of a stack, a water tank, and a radiator coupled to a fan, was built on the Simulink platform. A model-based controller consisting of nonlinear feedforward and LQR state feedback was added to the model. The simulation results showed that the controlled system performed satisfactorily. Also, when applied on a real system, the controller worked out well. Data collected from the city bus show that the temperature of the stack is kept in a range within +/- 0.5 degrees C. Copyright (C) 2015, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.