Fuel cells that are being developed as auxiliary power units (APUs) for DOD and civilian vehicles, aircrafts and ships require low sulfur fuels, usually less than 1 ppm. Logistic fuels and jet fuels often contain orders of magnitude higher sulfur levels (1000 to 10000 ppm). Most of the on-board or field-deployable fuel desulfurizers under development involve sorbent beds that undergo cyclic sorption and regeneration steps requiring thermal cycling and fuel wastage in combustion during regeneration. Intelligent Energy, Inc. (IE) has developed a novel, compact desulfurization technique involving membrane separation without loss of fuel. IE desulfurization process separates the fuel into a clean fuel for fuel cell subsystem and a sulfur-enriched fuel for the main power plant – ICE or combustion turbines. This paper presents process design aspects as well as the experimental data from the IE membrane desulfurization process on Jet fuels.