A system and method for estimating the amount of hydrogen and/or nitrogen in a fuel cell stack and stack volumes at system start-up and shut-down. The method defines the fuel cell stack and stack volumes as discrete volumes including an anode flow-field and anode plumbing volume, a cathode flow-field volume and a cathode header and plumbing volume. The method estimates the amount of hydrogen and/or nitrogen in the anode flow-field and anode plumbing volume, the cathode flow-field volume and the cathode header and plumbing volume when the fuel cell system is shut down, during a first stage when the hydrogen partial pressure between the anode and cathode is not in equilibrium and during a second stage when the hydrogen partial pressure between the anode and cathode is in equilibrium by considering various flows into and out of the volumes.