A fuel cell system in a vehicle includes a fuel cell stack and a cooling system for cooling the fuel cell stack. The cooling system has a radiator and at least one pump configured to supply coolant to the fuel cell stack. A controller operates the cooling system to actively cool the fuel cell stack while the vehicle is shut down in response to conditions indicating that the next time the vehicle will be started, it will be a cold start. The controller can then, subsequent to initiating the cooling, purge the fuel cell stack.