A pulse width modulation (PWM) fan controller includes a sensor, a generator, a selector, and a multiplexer. The sensor is configured for sensing a current temperature of an electronic device. The generator is configured for generating different PWM signals, each of which is suitable for regulating the rotational speed of a fan for dissipating heat for the electronic device of a corresponding temperature. The selector is configured for generating a selection control signal based upon the current temperature of the electronic device. The selection control signal is used for selecting a PWM signal corresponding to the current temperature of the electronic device from the PWM signals from the generator. The multiplexer is configured for performing the selection of the PWM signal.