The growing trend of the cruise ship industry, together with increasing concerns over its impact on the environment, makes these ships a much relevant target for the efforts toward increasing ship energy efficiency, thus ultimately reducing fuel consumption and emissions of carbon dioxide and other air pollutants. In a context of rising discussions concerning the use of cleaner fuels such as LNG and methanol in shipping, fuel cells are expected to become an increasingly viable solution for onboard power generation. In particular, solid oxide fuel cells (SOFC) can offer high electrical efficiency, power density and reliability with the possibility of combined heat, hydrogen and power production, which make them suitable for energy-intensive applications with a diverse demand (e.g., cruise ships) by integrating other complementary technologies. In this paper, we investigate the potential for energy and emission savings in relation to the use of SOFCs on cruise ships. Given the limited ability of SOFCs to deal with fast load changes and start/stop cycles, the SOFCs are expected to tackle the baseload, while a combination of batteries and internal combustion engines are complementary for handling peak loads. The proposed system is tested and optimized for a case study of a cruise ship operating in the Baltic Sea. Based on reference operational profiles for heat and electricity demand, the design of the system is optimized. The system proves particularly performant, with an overall efficiency close to 70% and a potential lifetime economic performance in line with conventional systems powered by Diesel engines.