A fan control system includes a fan and a fan control circuit. The fan control circuit includes a connector, a control unit, a switch unit, and a delay unit. The control unit is connected to the connector to receive a rotation speed control signal, and connected to the fan. The switch unit is connected to the connector to receive a voltage signal, and connected to the control unit. The delay unit is connected to the connector to receive the rotation speed control signal, and connected to the switch unit. When the delay unit receives the rotation speed control signal, the delay unit outputs a control signal to turn on the switch unit after a time delay, the voltage is transmitted to the control unit through the switch unit, the fan operates, the control unit controls rotation speed of the fan according to the rotation speed control signal.