In order to promote low-carbon fuels such as hydrogen to decarbonize the maritime sector, it is crucial to promote clean fuels and zero-emission propulsion systems in demonstrative projects and to showcase innovative technologies such as fuel cells in vessels operating in local public transport that could increase general audience acceptability thanks to their showcase potential. In this study, a short sea journey ferry used in the port of Genova as a public transport vehicle is analyzed to evaluate a ”zero emission propulsion” retrofitting process. In the paper, different types of solutions (batteries, proton exchange membrane fuel cell (PEMFC), solid oxide fuel cell (SOFC)) and fuels (hydrogen, ammonia, natural gas, and methanol) are investigated to identify the most feasible technology to be implemented onboard according to different aspects: ferry daily journey and scheduling, available volumes and spaces, propulsion power needs, energy storage/fuel tank capacity needed, economics, etc. The paper presents a multi-aspect analysis that resulted in the identification of the hydrogen-powered PEMFC as the best clean power system to guarantee, for this specific case study, a suitable retrofitting of the vessel that could guarantee a zero-emission journey.