The maritime sector forecasts that ammonia will play a pivotal role in decarbonizing ships since it does not emit carbon dioxide (CO₂). Nevertheless, burning ammonia in ICE produces nitrogen oxides (NO₂ and N₂O), which are GHG more dangerous than CO₂. The use of Proton Exchange Membrane Fuel Cell (PEM) systems instead of ICE avoids the emissions of harmful compounds. In this study, a PEM system is considered for the electric power generation onboard a 63 m length mega-yacht, replacing a traditional MGO gen-set. The pure hydrogen required for fuelling the PEM is produced through an ammonia decomposition reactor and a purification system, to be installed onboard as well. It results that an ammonia processing system for generating hydrogen requires additional power, in this case study is in the range of 360–475 kWe, and it is heavier and bulkier than the gen-set. Despite these cons, its installation onboard seems to be feasible and it does not involve significant modifications to the original configuration of the mega-yacht. The ammonia-fuelled mega-yacht reduces the original duration of navigation from 11 to about 5 days, nevertheless, this value appears still adequate considering the innovative solution at zero-emission proposed.