The first station at Williams Junction was built by Morrison-Knudsen for the Atchison, Topeka & Santa Fe Railway as part of construction of the Crookton Cutoff: a new 44-mile (71 km) stretch of the Southern Transcon built to avoid the sharp curves and steep gradients of the existing line between Williams and Ash Fork.

[7] Both Williams stations closed on April 30, 1969 following the Santa Fe's discontinuation of passenger services to the Grand Canyon and Phoenix via the Peavine.

[2] Unlike its predecessor, the modern Williams Junction had no station building or facilities, and no access for private motor vehicles.

[11] Passengers could only access the Williams Junction station using an Amtrak Thruway shuttle operated by the Grand Canyon Railway.

[4] To accommodate passengers requiring a connection to the Grand Canyon, Amtrak introduced a new Thruway bus service to and from Flagstaff.