Abstract High-speed passenger vessels (HSPVs) play an important role in coastal regions due to their high energy consumption and emissions. This study develops an optimal energy management system (EMS) for a zero-emission hybrid power system, powered by a fuel cell (FC) and a battery energy storage system (BESS). The global optimal solution for loading the FC and operating the BESS is computed using a linear programming (LP) approach, assuming a priori knowledge of the complete operational profile. Since the global solution is not realizable in an onboard EMS, the main objective of this paper is to develop an algorithm for real-time application. A multi-horizon model predictive control (MH-MPC) algorithm is applied to a model of the power system to solve the optimization problem with a prediction mechanism over the entire route. This approach is benchmarked against the global LP solution to evaluate the effectiveness of the proposed EMS. The results highlight the potential of the MH-MPC approach for achieving a near-optimal EMS in a zero-emission HSPV.