Maritime transportation is the most efficient transportation type. Despite, maritime transportation is an effective way to transport goods and passengers, fossil fuels are still in use. Ammonia and hydrogen are promising alternative fuels for the complete decarbonization of maritime transportation with their zero-carbon content and they are also suitable fuels for fuel cells. In this study, ammonia and hydrogen were compared by using safety, cost, commercial constraint, sustainability, and environmental impact criteria to find which one is the best possible fuel option for fuel cells in terms of use for the shipping industry.