A method for controlling the operation of a brushless DC fan for cooling heat generating components of a system is provided. The method includes providing a system temperature signal indicative of a system temperature and providing an intelligent shutdown enable signal. The system temperature signal is compared with a shutdown temperature signal if the intelligent shutdown enable signal has a first value. The shutdown temperature signal is representative of a shutdown temperature value. The fan is operated at a generally temperature proportional speed after comparing the system temperature signal with the shutdown temperature signal if the system temperature as indicated by the system temperature signal is greater than the shutdown temperature value as indicated by the shutdown temperature signal. A shutdown mode is entered by the fan after comparing the system temperature signal with the shutdown temperature signal if the system temperature as indicated by the system temperature signal is less than the shutdown temperature value as indicated by the shutdown temperature signal. The system temperature signal is compared with the shutdown temperature signal after entering the shutdown mode by the fan. Operation of the fan is initiated if the system temperature as indicated by the system temperature signal is greater than the shutdown temperature value as indicated by the shutdown temperature signal and the fan is in the shutdown mode.