A process and system for separating a fuel stream containing a low concentration of sulfur compounds from a primary fuel stream is disclosed. The process includes isolating a stage-one permeate stream and a stage-one retentate stream from the primary fuel stream, evaporating the stage-one permeate stream at a vacuum, and isolating a stage-two permeate stream and a stage-two retentate stream from the stage-one permeate stream. The stage-two retentate stream is a fuel stream containing low concentrations of sulfur compounds. The system includes a fuel supply, a stage-one separator for separating a fuel stream into a stage-one permeate stream and a stage-one retentate stream, a stage-two separator, a first supply line connecting a portion of the fuel supply to the stage-one separator, and a second supply line connecting the stage-one separator permeate stream to the stage-two separator. The stage-two separator isolates the stage-one separator permeate stream into a stage-two permeate stream and a stage-two retentate stream.