A system and method of spread-spectrum fan control for an air-cooled system is provided for reducing the vibrational and acoustical noise associated with the air-cooled system. The method includes generating a first control signal that controls a blade-passing frequency of a first cooling fan and a second control signal that controls a blade-passing frequency of a second cooling fan, wherein the first and second control signals may be pulse width modulated (“PWM”) signals. One or more noise generators independently vary duty cycles for the first and second PWM signals within a range around respective first and second blade-passing frequency set points. As a result, the blade-passing frequencies for the first and second cooling fans are independently and randomly modulated within a range around the respective first and second blade-passing frequency set points.