PROBLEM TO BE SOLVED: To provide, in the desulfurization of sulfur compound by using ozone, a method and apparatus for desulfurizing sulfur compound in fuel that can efficiently desulfur the sulfur compound.SOLUTION: The method for desulfurizing sulfur compound in fuel includes: adding an oxidation catalyst supporting mesoporous silica as well as charging a sulfur compound-containing fuel into a reaction tank 12; and feeding an ozone generated by an ozone generator 14 into the reaction tank 12 through an ozone feed line 16, to react the sulfur compound and ozone in the presence of oxidation catalyst supporting mesoporous silica and oxidate the sulfur compound to a sulfur oxide.