Organic nitrogen and sulfur compounds were separated from model fuels with supported liquid membranes using ionic liquids, based on 1-alkyl-3-methylimidazorium and quaternary ammonium salts. The organic nitrogen and sulfur compounds selectively permeated the membranes. Liquid membranes that used more hydrophilic ionic liquids yielded higher selectivity. The ionic liquids were retained in membrane pores after ten times repeated experiments. Application of supported liquid membranes based on ionic liquids has potential for the separation process of organic nitrogen and sulfur compounds from the fuels.