The accident happened about 4pm on the Finke Track - where the Finke Desert Race is held each year - 35 kilometres south of the Stuart Highway intersection.
The 27-year-old quad bike rider died at the scene.
The motorbike rider, 24, was taken to Alice Springs Hospital in a serious condition.
He has since been flown interstate for treatment.
Major Crash Detectives remain on the scene and motorists have been told to avoid the area and follow all traffic directions.
A report will be prepared for the Coroner.
