A fuel cell system is provided having a fuel cell stack including a plurality of fuel cells. The fuel cell system includes an anode supply manifold in fluid communication with the plurality of fuel cells, the anode supply manifold adapted to deliver a anode supply stream to the plurality of fuel cells; an anode exhaust manifold in fluid communication with the anodes of the plurality of fuel cells, the anode exhaust manifold adapted to receive an anode exhaust stream from the plurality of fuel cells; a first valve in fluid communication with the anode supply manifold; and a second valve in fluid communication with the anode exhaust manifold. A method of starting the fuel cell system is also provided. The fuel cell system and method militates against a non-uniform distribution of the anode supply stream to the anodes of the plurality of fuel cells.