As regulations on air pollutants emitted by ships are strengthened, the demand for the development of eco-friendly alternative fuels is increasing. Bio-heavy oil (BHO), a by-product of biodiesel manufacturing, is an eco-friendly fuel produced from biodiesel pitch. This study verified the possibility of using BHO as an eco-friendly alternative fuel for ships by analyzing the environmental and economic effects of using BHO in small ships. Compared to bunker A, BHO showed NOx emissions that increased by 5%, but SOx 9%, total hydrocarbons 9%, CO 4%, and CO 2 emissions decreased by 6%, confirming the effect of reducing greenhouse gases and air pollutants. There was also no difference in the engine performance. Furthermore, no discoloration, sludge generation, or fuel separation was observed when the fuel was stored for 90 days. During a total of 120 h of maritime demonstration, there were no engine problems and almost no sediment was produced. It has been proven to be a suitable replacement for ship fuel. The use of the BHO generated social benefits worth $ 2,256,749 per year. Therefore, it is necessary to promote the use of BHO in small ships.