An obstruction is removed from a computer system cooling fan by manipulating fan rotation. When a fan obstruction is detected, the fan is stopped. If the obstruction is caused by an object that was drawn toward the fan intake, such as a sheet of paper, this operation may clear the obstruction. The fan may also be reversed to attempt to blow the obstruction clear of the fan. Thereafter, the fan is returned to normal operation and is monitored to determine whether the obstruction was removed. If the fan is still obstructed, these steps can be repeated. If the attempts to clear the obstruction are unsuccessful, then the computer system operator or management software can be signaled.