Fuel cells as clean power sources are very attractive for the maritime sector, which is committed to sustainability and reducing greenhouse gas and atmospheric pollutant emissions from ships. This paper presents a technological review on fuel cell power systems for maritime applications from the past two decades. The available fuels including hydrogen, ammonia, renewable methane and methanol for fuel cells under the context of sustainable maritime transportation and their pre-processing technologies are analyzed. Proton exchange membrane, molten carbonate and solid oxide fuel cells are found to be the most promising options for maritime applications, once energy efficiency, power capacity and sensitivity to fuel impurities are considered. The types, layouts and characteristics of fuel cell modules are summarized based on the existing applications in particular industrial or residential sectors. The various research and demonstration projects of fuel cell power systems in the maritime industry are reviewed and the challenges with regard to power capacity, safety, reliability, durability, operability and costs are analyzed. Currently, power capacity, costs and lifetime of the fuel cell stack are the primary barriers. Coupling with batteries, modularization, mass production and optimized operating and control strategies are all important pathways to improve the performance of fuel cell power systems.