Fuel cell-battery electric drivetrains are attractive alternatives to reduce the shipping emissions. This research focuses on emission-free cargo vessels and provides insight on the design, lifetime operation and costs of hydrogen-hybrid systems, which require further research for increased utilization. A representative round trip is created by analysing one-year operational data, based on load ramps and power frequency. A low-pass filter controller is employed for power distribution. For the lifetime cost analysis, 14 scenarios with varying capital and operational expenses were considered. The Net Present Value of the retrofitted fuel cell-battery propulsion system can be up to $ 2.2 million lower or up to $ 18.8 million higher than the original diesel mechanical configuration, highly dependent on the costs of green hydrogen and carbon taxes. The main propulsion system weights and volumes of the two versions are comparable, but the hydrogen tank (68 tons, 193 m³) poses significant design and safety challenges.