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