A system and method for quantifying an anode leak location in a fuel cell system. The system and method include determining there is a leak in an anode sub-system of a fuel cell stack and estimating a first effective leak area using a first leak flow value and first operating parameters. The system and method also include increasing airflow to a cathode side of the fuel cell stack and estimating a second leak effective area using a second leak flow value and second operating parameters. The system and method further include comparing the first leak effective area to the second leak effective area and determining an anode outflow leak location based on the comparison between the first and second leak effective areas.