Fuel cell systems will be applied as non-regenerative power source in HERMES and as regenerative power supply in future space stations. To support project development and engineering tasks flexible software is needed for simulation and analysis of such systems.A simulation program, called SANFU (System ANalyzer for FUel cells) for low temperature fuel cells has been developed, which supports a modular model construction. The current configuration of the program includes simulation of transient thermal boundary conditions, transient electrical interface data, several operating options and different control logics. For HERMES fuel cell system simulation three standard fuel cell configurations are currently being simulated: immobile electrolyte fuel cells, mobile electrolyte (KOH) fuel cells and solid polymer electrolyte fuel cells.Test results for different load cases and transient boundary conditions are quoted. The general design, input and output capabilities, future extensions and applications are discussed.