Over the years, a number of schools entered and left the league. In 1988, Eastern Utah cancelled its football program and left the league. Its place was taken in 1993 by New Mexico Military Institute. Eastern Arizona left the WSFL in 1994, but rejoined the following year. New Mexico Military left the league in 1996, but rejoined in 2001. Pima Community College joined the WSFL in 2001. In 2002, Ricks College cancelled all sports and left the WSFL, after changing its name to Brigham Young University–Idaho. In 2006, Dixie State left the league when the school moved to the NCAA Division II level. New Mexico Military left the WSFL for the Southwest Junior College Football Conference (SJCFC) following the 2015 season.
All of the schools in Arizona canceled football following the 2018 season, leaving only Snow College, which is now an NJCAA independent.
The conference game between Glendale and Eastern Arizona was ruled a no-content after the game was ended at halftime following a brawl between the two teams.