A cooling system is provided for an engine. The cooling system may have an air cooler configured to cool intake air being supplied to the engine. The cooling system may also have a sensor configured to generate a temperature signal indicative of a temperature of the intake air and a fan in proximity to the air cooler. The cooling system may further have a controller in communication with the sensor and the fan. The controller may be configured to cause the fan to operate at a speed that is a function of the temperature signal when the temperature of the intake air is above a threshold temperature. The controller may further be configured to selectively cause the fan to pulse when the temperature of the intake air drops below the threshold temperature.