A system for producing an auxiliary fuel stream containing a low concentration of sulfur compounds from a primary fuel stream includes a first separation stage to separate a portion of a primary fuel stream into a first vapor permeate stream and a first retentate stream, a first separation stage partial condenser connected to the first vapor permeate stream condensing a portion of the first vapor permeate stream into a first liquid stage stream and a first vapor stage stream, and a second separation stage partial condenser condensing a portion of the first vapor stage stream into a second liquid stage. The first vapor permeate stream is preferable sent through a vapor phase reactive desulfurization catalyst reactor to condition any sulfur compounds present into species that can be easily separated from the fuel stream. The process includes isolating a first vapor permeate stream and a first retentate stream from a primary fuel stream by passing a portion of the primary fuel stream through a first membrane separation stage, condensing a portion of the first vapor permeate stream in a first separation stage partial condenser into a first liquid stage stream and a first vapor stage stream, and passing the first vapor stage stream through a desulfurization reactor. The stream may then be processed through a sorbent bed to effectively remove the sulfur compounds.