A system and method for cleaning sulfur and other pollutants from bunker oil to be used for fuel in large cargo ships is described. Preferably, the system includes two or more stages having a mixer to create an emulsion of oil and water. One or more treatment chemicals are added to the water before it is mixed with the oil in order to assist in separating the sulfur from the oil and freeing it up so that it can combine with various other molecules present in the water or be dissolved in the water. The emulsion may pass through a microcavitation chamber as well as an electrolysis reactor chamber in order to further clean the fuel oil by removing additional sulfur content. The clean fuel is sent to a fuel service tank for use in a diesel engine combustion cycle.