The endurance is one of the most important performances of the Unmanned Underwater Vehicles. Especially power determines the range and mission characteristics of the vehicle. A new sources of energy dedicated to underwater applications are developed. A simulation model of an energy system, based on fuel cells, designed to supply Autonomous Underwater Vehicles is presented in the paper. The model was implemented in MATLAB/Simulink environment after considerable simplifications. The developed simulator of the PEM Fuel Cell energy system cab be a useful tool to analyze the main electrical quantities under changing working conditions.