The use of hydrocarbon fed fuel cell systems including a fuel processor can be an entry market for this emerging technology avoiding the problem of hydrogen infrastructure. This article presents a 1 kW low temperature PEM fuel cell system with fuel processor, the system is fueled by a mixture of methanol and water that is converted into hydrogen rich gas using a steam reformer. A complete system model including a fluidic fuel processor model containing evaporation, steam reformer, hydrogen filter, combustion, as well as a multi-domain fuel cell model is introduced. Experiments are performed with an IDATECH FCS1200™ fuel cell system. The results of modeling and experimentation show good results, namely with regard to fuel cell current and voltage as well as hydrogen production and pressure. The system is auto sufficient and shows an efficiency of 25.12%. The presented work is a step towards a complete system model, needed to develop a well adapted system control assuring optimized system efficiency.