Abstract The maritime sector is under increasing pressure to decarbonize owing to its considerable contribution to global greenhouse gas (GHG) emissions. Among emerging energy carriers, hydrogen and ammonia have attracted significant attention due to their potential for zero-carbon propulsion when employed with fuel-cell technologies. This study undertakes a comprehensive life cycle cost analysis (LCCA) to evaluate the economic feasibility of hydrogen- and ammonia-fuelled systems for short-sea ferry operations in Norway. Five propulsion configurations are examined: blue and green hydrogen in proton-exchange membrane fuel cells (PEMFCs), blue and green ammonia in solid oxide fuel cells (SOFCs), and a conventional diesel system serving as the baseline. The case study focuses on the ferry Baronessen, operating on the Oslo Fjord between Aker Brygge and Nesoddtangen. In this study, life cycle cost efficiency is measured through net present value (NPV) of costs, where lower NPV indicates higher cost efficiency. Results indicate that the diesel-powered system remains the most cost-efficient, exhibiting a NPV of €1.03 million. The blue hydrogen PEMFC configuration follows with an NPV of €1.90 million, while green hydrogen reaches €2.23 million. In contrast, blue and green ammonia in SOFCs incur 2.7–3.2 times higher costs than diesel. Sensitivity analyses reveal that green hydrogen becomes cost-competitive once its price falls to approximately €2.19/kg. The findings underscore that hydrogen-fuelled PEMFCs are the most economically promising option for near-term short-sea shipping, whereas ammonia-fuelled SOFC systems remain financially unviable under current cost conditions.