Solid-Oxide-Fuel-Cell (SOFC) stacks respond in seconds to changes in load while the balance of plant subsystem (BOPS) responds in times several orders of magnitude higher. This dichotomy diminishes the reliability and performance of SOFC electrodes with changes in load. In the same manner current and voltage ripples which result from particular power electronic subsystem (PES) topologies and operation produce a negative effect on the SOFC stack subsystem (SS) performance. The difference in transient response among the sub-systems must be approached in a way which makes operation of the entire system not only feasible but ensures that efficiency and power density, fuel utilization, fuel conversion, and system response are optimal at all load conditions. Thus, a need exists for the development of transient component- and system-level models of SOFC based auxiliary power units (APUs), i.e. coupled BOPS, SS, and PES, and the development of methodologies for optimizing subsystem responses and for investigating system-interaction issues. In fact the transient process occurring in a SOFC based APU should be systematically treated during the entire creative process of synthesis, design, and operational control, leading in its most general sense to a dynamic optimization problem. This entails finding an optimal system/component synthesis/design, taking into account on- and off-design operation, which in turn entails finding an optimal control strategy and control profile for each sub-system/component and control variable. Such an optimization minimizes an appropriate objective function while satisfying all system constraints. A preliminary set of chemical, thermal, electrochemical, electrical, and mechanical models based on first principles and validated with experimental data have been developed and implemented using a number of different platforms. These models have been integrated in order to be able to perform component, subsystem, and system analyses as well as develop optimal syntheses/designs and control strategies for transportation and stationary SOFC based APUs. Some pertinent results of these efforts are presented here.