A system and method for detecting small hydrogen leaks in an anode of a fuel cell system. The method includes determining that a shut-down sequence has begun, and if so, deplete the cathode side of a fuel cell stack of oxygen. The method then increases the pressure of the anode side of the fuel cell stack to a predetermined set-point, and monitors the pressure decay of the anode side of the stack. The method compares the rate of pressure decay to an expected pressure decay rate, and if the measured pressure decay rate exceeds the expected pressure decay rate by a certain threshold, determines that a potential leak exists.