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The solid oxide fuel cell (SOFC) system has emerged as an important technology for automotive and stationary applications. Modeling and simulation of the SOFC system have been utilized as an integral tool in an accelerated joint SOFC system development program. Development of unique modeling approaches and their results are discussed and compared with experimental performance. One dimensional system level analysis using Aspen with an embedded stack electrochemical model was performed resulting in effective sub-system partitioning and requirements definition. Further, a three-dimensional integrated electrochemical / thermal / computational fluid dynamics analysis of steady-state operation was employed. The combination of one-dimensional and three-dimensional environments led to effective performance projection at all levels in the system, resulting in optimization of overall system performance early in the design cycle.