If the fuse is blown replace it and see what happens.
Bmw e39 aux fan relay location.
If the fuse is not blown the most likely fault is the final stage unit or the fan motor.
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On all bmw models up through the late 90s the auxiliary or main fan is controlled by one or two thermostatic switches that are mounted into the radiator side or bottom tanks.
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There is no engine driven mechanical fan.
For the bmw e39 1996 1997 1998 1999 2000 2001 2002 2003 model year.
The fan is mounted between the radiator and the engine and is the main engine cooling fan.
Bmw models that do have an engine driven fan will also have an electric fan mounted in front of the radiator known as the auxiliary cooling fan.
This is the electrical fuse and relay box under the plastic cover in the passenger side rear of the engine bay.
The bentley repair manual shows the location on page ecl 20.
Fuse box in passenger compartment bmw e39.