The Mississippi Valley Conference was formed in 1989 to accommodate for the growing attendance in schools in traditional
rural-based conferences and shorten travel distances for its members. Holmen and Onalaska joined from the Coulee Conference, Sparta and Tomah from the South Central Conference, and
La Crosse Central High School and
Logan High School from the Big Rivers Conference. Shortly after, in 1997,
Aquinas High School joined from the
Central Wisconsin Catholic Conference of the
Wisconsin Independent Schools Athletic Association, a private school athletic league, to become the conference's seventh member. It is the second high school athletic conference in Wisconsin to carry this name, the
previous incarnation was based in west central Wisconsin and was in existence from 1933 to 1965. In 2014,
West Salem began competition in the Mississippi Valley Conference for football only, remaining in the
Coulee Conference for all other sports. Aquinas left the MVC's football roster in 2019 when they joined the
Southwest Wisconsin Activities League as associate members for that sport. The next year, a comprehensive realignment of Wisconsin high school football conferences was implemented by the WIAA with input from the
Wisconsin Football Coaches Association to run on a two-year cycle. All six of the MVC's public high schools (Central, Holmen, Logan, Onalaska, Sparta and Tomah) remained in the conference with associate members River Falls (Big Rivers) and West Salem (Coulee) filling out the ranks. River Falls and West Salem returned to their respective conferences for the 2022-2023 realignment cycle with two schools from the
Badger Conference (
Baraboo and
Reedsburg) replacing them. This alignment will stay in effect through at least the 2026-2027 competition cycle. == Sports sponsored ==