A purging system for removing oxygen from a fuel cell system during a shutdown period for the fuel cell system. The purging system includes a separator having an inlet and an outlet; a first exhaust line for communicating a first exhaust gas stream from an outlet of the fuel cell system to the separator inlet during the shutdown period of the fuel cell system; and a second exhaust line for communicating a second exhaust gas stream to an inlet of the fuel cell system for delivering the second exhaust gas stream to the fuel cell system during the shutdown period. The separator removes oxygen from the first exhaust gas stream such that the first stream nitrogen molar volume is lower than the second steam nitrogen molar volume and the first stream oxygen molar volume is higher than the second stream oxygen molar volume.