This study proposes a feasible solution for boil-off gas (BOG) treatment to facilitate NH3 fuel use by ocean-going ships, which is currently considered an alternative fuel for ships. Two systems were designed and analyzed for BOG in IMO Type-A NH3 fuel storage tanks for 14,000 TEU container ships. First, BOG lost inside the storage tank minimized economic losses through the onboard re-liquefaction system. The total energy consumed by the system to process NH3 gas generated in the fuel tank at 232.4 kg/h was 51.9 kW, and the specific energy consumption (SEC) was 0.223 kWh/kg. Second, NH3 was supplied to the direct Low-Pressure Selective Catalytic Reduction (LP-SCR) system to treat marine pollutants generated by combustion engines. The feasible design point was determined by calculating the NH3 feed flow rate using three methodologies. The energy consumed by the direct LP-SCR system was 3.89 and 2.39 kW, and the SEC was 0.0144 at 0.0167 kWh/kg at 100% and 25% load, respectively. The feasibility was indicated via economic analysis. Depending on the life cycle cost, the competitiveness of the re-liquefaction system depends on the price of NH3, where a higher price yields a more economical solution. In conclusion, the direct LP-SCR system has a low overall cost because of its low energy consumption when supplying NH3 and its reduced amount of core equipment.