Global endeavors to reduce emissions in the shipping industry are accelerating the interest in fuel cell systems. This paper explores the application of different fuel cell types (LT-PEMFC, HT-PEMFC and SOFC) in combination with different fuels (LH2, LNG,MeOH and NH3) in expedition cruise ships. An impact model is developed for the first design phase. The goal of this paper is to evaluate the impact of the combination of fuel cell system implementation and operational profile on expedition cruise vessels. Impact is expressed in ship size, capital cost, operational cost and emissions. The model takes into account: fuel storage, on-board fuel processing, fuel cell system characteristics, balance of plant components, fuel cost over operational lifetime and all onboard emissions. In the research, seven different fuel cell systems and three different hybridization strategies are considered. For the six best performing combinations of fuel cell system and hybridization strategy, the range, endurance and capacity requirements are systematically varied to determine whether the best performing option depends on these requirements. Finally, hybrid option 2 (using diesel generators to support during long transits) combined with a methanol fueled LT-PEMFC system results in the lowest newbuild price. This option does comply with emission regulations and CO2 goals for 2030. Hybrid option 2 combined with an LNG fueled LT-PEMFC system results in the lowest total cost (newbuild price and fuel cost). This option does comply with emission regulations, but does not meet CO2 goals for 2030. When it is desired to reach this CO2 target, hybrid option 2 with methanol fueled LT-PEMFC is also recommended from a total cost perspective.