A fuel cell system includes a fuel cell stack, an anode reactant source and a shut-off valve that selectively prohibits anode reactant flow from the anode reactant source to the fuel cell stack through a conduit. A control module initiates closure of the shut-off valve to prohibit anode reactant flow through the conduit and determines a shutdown schedule based on a residual mass of the anode reactant within the conduit. The control module operates the fuel cell system using the residual mass and based on the shutdown schedule.