Today’s remarkable challenge of maritime transportation industry is the detrimental contamination generation from fossil fuels. To tackle such a challenge and reduce the contribution into air pollution, different power solutions have been considered; among others, hybrid energy-based solutions are powering many ferry boats. This paper introduces an energy management strategy (EMS) for a hybrid energy system (HES) of a ferry boat with the goal to optimize the performance and reduce the operation cost. HES considered for the ferry boat consists of different devices such as proton exchange membrane fuel cell (PEMFC), LI-ION battery bank, and cold ironing (CI). PEMFC systems are appropriate to employ as they are not polluting. The battery bank compensates for the abrupt variations of the load as the fuel cell has a slow dynamic against sudden changes of the load. Also, CI systems can improve the reduction of the expenses of energy management, during hours where the ferry boat is located at the harbor. To study the performance, cost and the pollution contribution CO2, NOX, SOX of the proposed hybrid energy management strategy (HEMS), we compare it against three various types of HEM from the state-of-the-art and also available rule-based methods in the literature. The analysis results show a high applicability of the proposed HES. All results in this paper have been obtained in the MATLAB software environment.