If it is a standard setup the extruder fan is always on when the power is on. It is not controllable.
But lets be sure..
There are normally two fans on the hot end, one is directed at the hot end cooling fins and is normally wired directly to power
The second fan is for part cooling and can be turn on/off etc
Some of the newer controllers do let you control both... depends what controller you have.
You can also hack on a mosfet and add this feature...