A fan controlling system and method is applicable to an electronic device with a fan for adjusting a temperature of the electronic device. The fan controlling system includes a plurality of temperature sensors installed in different regions inside of the electronic device for sensing temperatures around the regions, a mapping table for mapping a plurality of temperature ranges onto a plurality of rotation speeds, and a processing module for comparing the temperatures sensed by the temperature sensors and controlling the fan to rotate according to one of the rotation speeds onto which the mapping table maps one of the temperature ranges within which a highest one of the sensed temperatures is. Therefore, the fan can operate stably and does not generate a loud noise even when its rotation speed is changing, and has a longer lifespan.