In this study, the environmental impacts of various alternative ship fuels for a coastal ferry were assessed by the life cycle assessment (LCA) analysis. The comparative study was performed with marine gas oil (MGO), natural gas, and hydrogen with various energy sources for a 12,000 gross tonne (GT) coastal ferry operating in the Republic of Korea (ROK). Considering the energy imports of ROK, i.e., MGO from Saudi Arabia and natural gas from Qatar, these countries were chosen to provide the MGO and the natural gas for the LCA. The hydrogen is considered to be produced by steam methane reforming (SMR) from natural gas with hard coal, nuclear energy, renewable energy, and electricity in the ROK model. The lifecycles of the fuels were analyzed in classifications of Well-to- Tank, Tank-to-Wake, and Well-to-Wake phases. The environmental impacts were provided in terms of global warming potential (GWP), acidification potential (AP), photochemical potential (POCP), eutrophication potential (EP), and particulate matter (PM). The results showed that MGO and natural gas cannot be used for ships to meet the International Maritime Organization’s (IMO) 2050 GHG regulation. Moreover, it was pointed out that the energy sources in SMR are important contributing factors to emission levels. The paper concludes with suggestions for a hydrogen application plan for ships from small, nearshore ships in order to truly achieve a ship with zero emissions based on the results of this study.