Recent advancements in fuel cell technology through the auspices of the Department of Energy, the National Aeronautics and Space Administration, and industry partners have set the stage for the use of solid oxide fuel cell (SOFC) power generation systems in aircraft applications. Conventional gas turbine auxiliary power units (APUs) account for 20% of airport ground-based emissions. Alleviating airport ground emissions will continue to be a challenge with increased air travel unless new technology is introduced. Mission fuel burn and emissions can be significantly reduced through optimal systems integration of aircraft and SOFC subsystems. This study examines the potential total aircraft mission benefits of tightly integrating SOFC hybrids with aircraft subsystems using United Technologies Corporation Integrated Total Aircraft Power Systems proprietary methodologies. Several system concepts for optimal integration of the SOFC stack with aircraft subsystems are presented and analyzed in terms of mission fuel burn for technologies commensurate with 2015 entry into service. The performance of various hybrid SOFC-APU system architectures is compared against an advanced gas turbine-based APU system. In addition to the merits of different system architectures, optimal SOFC system parameter selection is discussed. The results of the study indicate that despite the lower power density of SOFC-based APU systems, significant aircraft fuel burn (5–7%) and emission reductions (up to 70%) are possible. The majority of the fuel burn savings are realized during aircraft ground operations rather than in-flight mission segments due to the greater efficiency difference between the SOFC system and the advanced APU technology.