The maritime sector forecasts that ammonia will play a pivotal role in decarbonizing ships since it does not emit carbon dioxide (CO2). Nevertheless, ammonia produces nitrogen dioxide (NO2) burning in ICEs, which contributes to smog and acid rains, being harmful to human health. Combustion also yields small amounts of nitrous oxide (N2O), a significantly more dangerous greenhouse gas than carbon dioxide. An option for eliminating harmful emissions is using fuel cell (FC) technology. In this study, a comparison has been made between three different FC technologies and the impact of their installation onboard ship of a 64 m length mega-yacht, replacing a traditional Marine Gas Oil (MGO) generating set. FCs considered are Proton Exchange Membrane Fuel Cell (PEMFC), Solid Oxide Fuel Cell (SOFC) and Alkaline Fuel Cell (AFC). FCs can be fuelled by ammonia directly, like SOFC and AFC, or indirectly, like PEMFC. In the latter case, ammonia works as a hydrogen carrier, therefore, an ammonia decomposition reactor and a purification apparatus are required onboard as well. The IPS electrical distribution is considered to allow different operating modes of the ship and to reach a zero-emission condition both in port and in navigation. To identify the best result for the mega yacht the effect of each solution on the general arrangement of the ship is discussed. The main outcomes are that, in the case of PEMFC, the hydrogen production from ammonia requires a bulky and heavy fuel processing system which must overcome some constrictions for the installation onboard. Furthermore, such a system requires additional power, up to 600 kWe, and the electrical balance must be adjusted. On the other hand, the PEMFC system has a very high-power density (2.5 kW/kg or 2700 kW/m3), even than a Genset, that make easy the installation onboard. SOFC and AFC do not require a fuel processing system since the high operating temperature (300-800 °C) allows the ammonia decomposition on the anode electrode, thus reducing the plant complexity and improving the overall efficiency. However, the gravity and volumetric power density are lower, about 0.02 kW/kg and 8 kW/m3 respectively, compared to the PEMFC requiring a modification of the general arrangement of the mega-yacht for the installation. The available volume for the storage tanks limited the amount of ammonia stored onboard to about 48 m3. In the case of PEMFC, this considerably affected the ship's autonomy: depending on the operating mode, the autonomy varies from 3 to 6 days. In the case of SOFC and AFC, it is possible to reach the Atlantic autonomy of about 12-14 days.