A fuel cell air supply system disposed in an enclosure. A blower discharge plenum for supplying air individually to various fuel cell functions via individual control valves is provided with an additional controllable purge valve connected to an exhaust port through a wall of the enclosure. At any desired time, the purge valve may be opened and the system process valves closed to draw fresh air into the enclosure and thereby purge stale gases within the enclosure to the exterior of the system. This function is especially useful just prior to start-up of the fuel cells of the system, and may also be used periodically after shut-down to maintain a desirably low temperature in the enclosure during cooling off of the fuel cell assembly.