This study performs energetic and exergetic comparisons between the steam methane reforming and steam methanol reforming technologies combined with HT-PEMFC and a carbon capture/liquefaction system for use in hydrogen-fueled ships. The required space for the primary fuel and captured/liquefied CO2 and the fuel cost have also been investigated to find the more advantageous system for ship application. For the comparison, the steam methane reforming-based system fed by LNG and the steam methanol reforming-based system fed by methanol have been modeled in an Aspen HYSYS environment. All the simulations have been conducted at a fixed Wnet, electrical (475 kW) to meet the average shaft power of the reference ship. Results show that at the base condition, the energy and exergy efficiencies of the methanol-based system are 7.99% and 1.89% higher than those of the methane-based system, respectively. The cogeneration efficiency of the methane-based system is 7.13% higher than that of the methanol-based system. The comparison of space for fuel and CO2 storage reveals that the methanol-based system requires a space 1.1 times larger than that of the methane-based system for the total voyage time, although the methanol-based system has higher electrical efficiency. In addition, the methanol-based system has a fuel cost 2.2 times higher than that of the methane-based system to generate 475 kW net of electricity for the total voyage time.