This study presents the techno-economic analysis of a 100 kWe Solid Oxide Fuel Cell (SOFC) system for maritime applications fueled by methane, methanol, diesel, ammonia, and hydrogen. Two system configurations are considered for each fuel considering cathode off-gas recirculation (COGR) implementation to improve waste heat recovery both in terms of quantity and quality. The economic benefit of COGR is verified for all fuels, especially for methanol, hydrogen, and diesel, which present Levelized Cost of Exergy (LCOEx) reductions of about 10%, 9%, and 6%, respectively. Ammonia and methanol have the lowest LCOEx of about 0.260 EUR/kWh and 0.270 EUR/kWh, respectively, while hydrogen has the highest LCOEx of about 0.430 EUR/kWh. The sensitivity analyses suggest that fuel purchase cost, stack lifetime, and annual interest rate are the three parameters with the highest influence on the system cost. Overall, ammonia and methanol are the most promising fuels.