A system and method for providing a fuel cell stack purge to remove excess water during system shut-down. A compressor is operated at a shut-down speed to force water out of the cathode flow channels and draw water through the membrane from the anode flow channels so that a desired amount of water is removed from the fuel cell stack without over drying the membrane. The cathode shut-down purge flow can be introduced in the forward or reverse direction. Further, the flow of hydrogen fuel can be directed so that it flows through the anode flow channels in an opposite direction to push water out of an anode outlet manifold into the anode flow channels so that it will also be drawn through the membrane by the cathode airflow. Finally, a brief rehydration step is added after the shut-down purge to achieve the desired water content in the cells.