A method for filling a fuel cell system with a fuel during start-up is disclosed, the method including the steps of providing a fuel cell stack having a plurality of fuels cells, each fuel cell having an active area, the fuel cell stack including an anode supply manifold and an anode exhaust manifold, the anode supply manifold and in fluid communication with a source of fuel; providing an anode sub-system in fluid communication with an anode side of the fuel cell stack; and supplying the fuel to the fuel cell stack substantially uniformly and substantially simultaneously to compress any fluids in the fuel cell stack into a volume between an end of each active area adjacent to the anode exhaust manifold and an outlet of the anode sub-system.