In this study, real voyage data and ship specifications of a general cargo ship are employed, and it is assumed that diesel generators are replaced with hydrogen proton exchange membrane fuel cells. The effect of the replacement on CO2, NOX, SOX, and PM emissions and the CII value is calculated. Emission calculations show that there is a significant reduction in emissions when hydrogen fuel cells are used instead of diesel generators on the case ship. By using hydrogen fuel cells, there is a 37.4% reduction in CO2 emissions, 32.5% in NOX emissions, 37.3% in SOX emissions, and 37.4% in PM emissions. If hydrogen fuel cells are not used instead of diesel generators, the ship will receive an A rating between 2023 and 2026, a B rating in 2027, a C rating in 2028–2029, and an E rating in 2030. On the other hand, if hydrogen fuel cells are used, the ship will always remain at an A rating between 2023 and 2030. The capital expenditure (CAPEX) and operational expenditure (OPEX) of the fuel cell system are USD 1,305,720 and USD 2,470,320, respectively, for a 15-year lifetime, and the hydrogen fuel expenses are competitive at USD 260,981, while marine diesel oil (MDO) fuel expenses are USD 206,435.