a system and method for correcting an estimation of nitrogen in an anode side of a fuel cell stack . the system includes a fuel cell stack and a pressure sensor for measuring pressure in an anode sub - system . the system also includes a controller configured to control the estimation of nitrogen permeation from the cathode side to the anode side of the stack , where the controller determines if the pressure in the anode sub - system equilibrates with atmospheric pressure in a shorter period of time after shutdown compared to the time necessary for the anode sub - system to reach approximately atmospheric pressure after a previous shutdown or calibrated time value , and corrects the estimation of nitrogen in the anode side of the stack if the pressure equilibrates in a shorter period of time .