At BMW AG in Munich high-temperature solid oxide fuel cells (SOFCs) are being developed as an auxiliary power unit (APU) for high-class car conveniences. Their design requires simulation of their thermo-electrochemical behaviour in all the conditions that may occur during operation (i.e. heat-up to about 600°C, start-up to operating temperature, energy-delivering and cool-down). A global thermo-electrochemical model was developed for the whole system and a three-dimensional geometry code was performed using MATLAB programming language. The problems in developing SOFCs are now so many and so different that a very flexible code is necessary. Thus, the code was not only designed in order to simulate each of the operating conditions, but also to test different stack configurations, materials, etc. In every event, the code produces a time-dependent profile of temperatures, currents, electrical and thermal power density, gases concentrations for the whole system. The heat-up and start-up simulations allow: (1) to evaluate the time the cell stack needs to reach operating temperature from an initial temperature distribution, (2) to check the steepest temperature gradients occurring in the ceramic layers (which result in material stresses) and (3) to obtain important information about the pre-operating strategy. Simulation of energy-delivering gives a detailed profile of the temperatures, currents, power density, and allows to define the guidelines in system-controlling. Simulation of cooling-down gives important advises about insulation designing. The aim of this work is to build up a tool to clearly individuate the best designing criteria and operating strategy during the development and the engineering of a SOFC system.