This paper introduces a formal approach allowing the performance evaluation of Flexible Manufacturing Systems (FMS) while considering the whole system behavior (operation, transport and preparation) as well as its possible components failure. The proposed approach is based on a generic Generalized Stochastic Petri nets (GSP-nets) model. The introduced GSP-net model represents the basic operation of the FMS elements (machines and material handling systems) as well as their fail and recovery aspects. The existing formal verification GSP-nets methods are exploited, and especially the state space generation and handling, in order to deduce a set of performance indicators helping the FMS designers when scheduling the production. Extracted indicators allow to enhance the decision process and the system efficiency. An important advantage of the introduced approach is that it is parameterized. Thus, it may be adapted to a large class of existing FMSs. The instantiation of the presented GSP-nets model to the specific features of the studied FMS is made by colored tokens.