This paper presents the application of Particle Swarm Optimization (PSO) algorithm for optimization of the Gas Turbine Engine (GTE) fuel control system. In this study, the Wiener model for GTE as a block structure model is firstly developed. This representation is an appropriate model for controller tuning. Subsequently, based on the nonlinear GTE nature, a Fuzzy Logic Controller (FLC) with an initial rule base is designed for the engine fuel system. Then, the initial FLC is tuned by PSO with emphasis on the engine safety and time response. In this study, the optimization process is performed in two stages during which the Data Base (DB) and the Rule Base (RB) of the initial FLC are tuned sequentially. The results obtained from the simulation show the ability of the approach to achieve an acceptable time response and to attain a safe operation by limiting the turbine rotor acceleration.