A server or other computing system contains a plurality of heat-generating electrical components and one or more cooling fans to dissipate heat from those components during operation. The fans are controlled by one or more fan controllers, which are programmed with an adaptive control algorithm to change the speed of each system cooling fan based on the needs of the components. The adaptive control algorithm is selected based on a detected configuration of the system's components, which may be detected upon startup of the system. During operation, a fan controller receives the component temperatures from one or more sensor and uses the algorithm to determine the fan speed. Thus, the system variably controls the speed of the fans based on the configuration of components housed in the server unit and on the current temperature of the components.