This study focuses on providing design guidelines for a vessel’s power-plant in the multi-megawatt range, equipped with a hybrid fuel cell and battery system. Background information is provided on the challenges to realizing such a system, spanning from a literature review on studies looking into energy management, to the technical limitations of state-of-the-art fuel cells and batteries. The central part of the work consists of the description of the model used to calculate the size of the hybrid power generating unit, including a case study on a single, real-world scenario. The Plant Analysis Balance with Operational Profile (PABOP) model, developed by the author and presented in the paper, is used to calculate the resources needed to retrofit a vessel operating on fossil fuels with a hybrid zero-emission power-plant. The model aim is to achieve a 1:1 replacement for diesel-electric configurations, both in terms of range and power, using fuel cell and battery power. In the case study, the model is applied to analyze the operational data of a double-ended ferry operating with diesel-electric propulsion. Emphasis is put on the I/O needed and produced by the model, and how this tool can be used by shipyard engineers to estimate the footprint required, the necessary storage capacity, lifetime of components and other parameters. The presented solutions could help manufacturers estimate the economical viability of hydrogen vessels, filling a gap in current maritime fleets where zero-emission systems are gaining increasing importance.