© 2022 Hydrogen Energy Publications LLCGlobal warming and greenhouse gas emissions are today's major challenges for sustainable industrial developments, and shipping is an important key element of the industrial chain. However, maritime transportation is responsible for 3.1% of total CO2 emissions worldwide, and International Maritime Organization estimates that it will continue to increase if no measure is taken. In this perspective, alternative fuels are promising solutions to reach the zero-carbon shipping aim. This paper investigates zero-carbon fuels and their power generation solutions to eliminate ship-sourced CO2 emissions. Hydrogen and ammonia are analyzed to use in a fuel cell according to five different criteria: safety, cost, storage, sustainability, and environmental impact. Criteria weightings are found according to expert points by using the analytic hierarchy process. While the safety and environmental impacts have a major effect on the results, sustainability, storage, and cost are lined up, respectively. A final comparison table is formed by changing weightings for each criterion regarding maritime industry conditions. Sensitivity analysis of the results is carried out with different scenarios to show the reliability of the handled analysis. As a result, ammonia is marginally showed better performance against hydrogen for shipping with applied criteria in this work. This study highlights that shipping has strong options such as ammonia and hydrogen on the road of decarbonization and ammonia can play an important role in the transition to zero-carbon shipping.