Due to constantly increasing electricity consumption, networks are becoming overloaded and unstable. Decentralization of power generation using small-scale local cogeneration plants becomes an interesting option to improve economy and energy reliability of buildings in terms of both electricity and heat. It is expected that stationary applications in buildings will be one of the most important fields for fuel cell systems. In northern countries, like Finland, efficient utilization of heat from fuel cells is feasible. Even though the development of some fuel cell systems has already progressed to a field trial stage, relatively little is known about the interaction of fuel cells with building energy systems during a dynamic operation. This issue could be addressed using simulation techniques, but there has been a lack of adequate simulation models. International cooperation under IEA/ECBCS/Annex 42 aims at filling this gap, and the study presented in this paper is part of this effort. Our objective was to provide the means for studying the interaction between a building and a fuel cell system by incorporating a realistic fuel cell model into a building energy simulation. A two-part model for a solid-oxide fuel cell system has been developed. One part is a simplified model of the fuel cell itself. The other part is a system level model, in which a control volume boundary is assumed around a fuel cell power module and the interior of it is regarded as a “black box.” The system level model has been developed based on a specification defined within Annex 42. The cell model (programed in a spreadsheet) provides a link between inputs and outputs of the black box in the system model. This approach allows easy modifications whenever needed. The system level model has been incorporated into the building simulation tool IDA-ICE (Indoor Climate and Energy) using the neutral model format language. The first phase of model implementation has been completed. In the next phase, model validation will continue. The final goal is to create a comprehensive but flexible model, which could serve as a reliable tool to simulate the operation of different fuel cell systems in different buildings.