In order to minimize the mass of a spaceplane, fuel cells are being used instead of batteries. For HERMES the development of a state of the art fuel cell system which can operate under micro-gravity conditions is under way.A modular simulation program SANFU (System Analyzer for FUel cells) has been developed and applied within the HERMES fuel cell project. All major parameters which influence the component or system performance are taken into account and have been simulated: temperatures, heat and mass flow, chemical reactions within the fuel cell, electrical interfaces and controller logic.The improved simulation program now includes analyses on component and/or system level, modular exchange of components such as fuel cell stack, heat exchangers, pumps, electrolyte regenerators, valves, sensors, system and component controllers, electrical and thermal bus, etc. The network topology can be changed for example in order to optimize the system configuration.Three different fuel cell systems are included in the standard program: immobile electrolyte, mobile electrolyte and ion exchange membrane fuel cells. To incorporate heat flux to external structural parts a software interface with the thermal analyzer ESATAN is provided.The program has been tested for HERMES fuel cell system simulation. Results of simulation for different load cases, transient boundary conditions as well as different control concepts are shown. The general design, input and output capabilities, future extensions and applications are discussed.