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Maintaining a fuel cell (FC) system in correct operating conditions when subjected to fast load changes requires good system control. The best results are typically achieved using model-based control strategies. This paper elaborates a control-oriented proton exchange membrane FC system model in two distinct steps. First, the FC auxiliary systems (i.e., air and hydrogen supply along with thermal management) are described in a state-space approach linking user input to FC operating conditions. A steady-state FC stack model then describes the effect of those operating conditions on system performance. The model then allows the implementation of advanced control strategies such as multivariable control with decoupling, actuator sensitivity analysis or maximum efficiency tracking algorithms.