A system according to the principles of the present disclosure includes a start-stop module, a pre-ignition risk module, and a cooling control module. The start-stop module stops and restarts an engine independent from an input received from an ignition system. The pre-ignition risk module monitors a risk of pre-ignition when the engine is restarted and generates a signal based on the risk of pre-ignition. The cooling control module controls a cooling system to circulate coolant through the engine when the engine is stopped in response to the risk of pre-ignition.