In this paper, a novel model for dynamic reliability analysis of a PEM fuel cell system is developed using Modelica language in order to account for multi-state dynamics and aging. The modelling approach constitutes the combination of physical and stochastic sub-models with shared variables. The physical model consist of deterministic calculations of the system state described by variables such as temperature, pressure, mass flow rates and voltage output. Additionally, estimated component degradation rates are also taken into account.The non-deterministic model, on the other hand, is implemented with stochastic Petri nets which represent different events that can occur at random times during fuel cell lifetime. A case study of effects of a cooling system on fuel cell performance was investigated. Monte Carlo simulations of the process resulted in a distribution of system parameters, thus providing an estimate of best and worst scenarios of a fuel cell lifetime.