A system and method for improving fuel cell system start-up reliability. The method includes determining if the resistance of the membranes in a fuel cell stack is too high, where the reliability of system start-up will be reduced, and if so, providing one or more remedial actions to help ensure that the start-up is more reliable. In one embodiment, the system and method determine that the fuel cell membranes are to dry based on whether a high frequency measurement of the fuel cell stack exceeds a predetermined HFR threshold. If the HFR threshold has been exceeded, a special start-up procedure is used that increases the reliability that the start-up will be successful using the remedial actions, such as reducing cathode airflow and turning on stack end cell heaters.