A system and method for drying a fuel cell stack after stack shutdown. In one embodiment, a cooling fluid is pumped through the fuel cell stack after the system is shutdown to use the heat still available in the cooling fluid immediately after shutdown to provide thermal equilibrium in the stack. In another embodiment, the heated cooling fluid still available immediately after system shutdown is sent through a cathode input gas heat exchanger so that drying air from the system compressor is heated by the cooling fluid before it enters the stack. In another embodiment, a separate heat exchanger is provided that receives the drying gas prior to it being sent into the fuel cell stack.