The creation of the MW was a delayed aftereffect of the 1996 NCAA conference realignment, which had initially been triggered two years earlier when the Big Eight Conference agreed to merge with four members of the Southwest Conference (SWC) to create the Big 12 Conference, which would begin competition in the 1996–97 school year.

The Western Athletic Conference, which had initially announced plans to expand beyond its then-current 10 members to at least 12, ended up with even more potential expansion prospects. Ultimately, the WAC took in three of the four SWC schools left out of the Big 12 merger—Rice University, Southern Methodist University (SMU), and Texas Christian University (TCU). Three other schools were added to bring the total membership to 16, namely Big West Conference members San Jose State University and UNLV, plus the University of Tulsa, an NCAA football independent and otherwise a member of the Missouri Valley Conference. The WAC's 16 teams were divided into four four-team "quadrants", two of which rotated between the Mountain and Pacific Divisions every two years. However, the newly expanded WAC was soon wracked by tension between the established and new members.^[2]

In spring 1998, BYU and Utah proposed a permanent split into two eight-team divisions. The proposal would have forced some schools into an unnatural alignment because of the geographic distribution of the conference.^[2] Air Force was the most strident opponent of this proposal, threatening to become an independent.^[2] Soon after the proposal by BYU and Utah, the presidents of Air Force, BYU, Colorado State, Utah, and Wyoming met at Denver International Airport to discuss their future, and they agreed to break away from the WAC to form a new conference.^[2] They invited the WAC members New Mexico, San Diego State, and UNLV to join them in what became the Mountain West Conference.

The next move for the MW came in 2005, when the conference added TCU, who had spent the previous four seasons in Conference USA(C-USA).