The Wisconsin Flyway Conference was formed in 2006, the result of a split of six schools from the East Central Flyway Conference (Horicon, Laconia, Lomira, Mayville, North Fond du Lac and St. Mary's Springs). These schools were previously in the conference's Rivers Division and were members of the original Flyway Conference before its merger with the East Central Conference. Kettle Moraine Lutheran in Jackson was the seventh original member of the Wisconsin Flyway Conference, having been displaced by the closing of the Parkland Conference the year prior. Winnebago Lutheran Academy in Fond du Lac joined as the conference's eighth member after the East Central Flyway was closed in 2007. Omro's entry into the Wisconsin Flyway Conference from the Eastern Valley Conference in 2010 brought membership to its high of nine schools. This mark was to be short-lived, as Horicon left to join the Trailways Conference in 2012. The membership roster was further decreased to seven schools in 2015 when Kettle Moraine Lutheran became members of the reconstituted East Central Conference. In 2021, Campbellsport exited the East Central Conference to become the Wisconsin Flyway Conference's eighth member. This figure increased back to nine in 2025, as St. Lawrence Seminary joined as a full member after having previously been an associate member in multiple sports.
Football-only alignment
In February 2019, in conjunction with the Wisconsin Football Coaches Association, the WIAA released a sweeping football-only realignment for Wisconsin to commence with the 2020 football season and run on a two-year cycle. The Wisconsin Flyway Conference was set to keep its seven-member all-sport lineup intact for football, with the early addition of Campbellsport as a football-only member for 2020 before attaining full membership in 2021. In the wake of the COVID-19 pandemic, the Wisconsin Flyway Conference postponed their football season until the alternate season in spring 2021. Ripon and Waupun joined as temporary members for the season, as they were the only schools in the East Central Conference that did not field football teams for the fall 2020 season. The Wisconsin Flyway Conference has maintained its eight-member roster for football through the 2026-2027 realignment cycle.
