Compliance with the future CO2 emission limits presents a major challenge for every industry, especially the naval sector. The maritime industry contributes strongly to the total global CO2 emissions being around 3.5% of the total ones since it still relies mainly on fossil fuels for propulsion purposes. To comply with these stringent limits one solution that is gaining interest is using hydrogen as an energy carrier. Specifically, the development of Proton Exchange Membrane (PEM) fuel cells for ships is of significant interest due to their basically non-existent CO2 emissions. However, the performance of PEMs depends strongly on the control strategy adopted in order to ensure high efficiency, reliability and durability as well as safe operation.