Central Wisconsin Christian joined the conference after leaving the East Central Flyway Conference in 2004, and two years later the Trailways Conference took three more former East Central Flyway schools into the fold: Lourdes Academy, Markesan and Oakfield. All three schools joined the North Division with Pardeeville moving over to the South Division to accommodate the expansion:[2]
North Division
South Division
Cambria-Friesland
Abundant Life Christian
Central Wisconsin Christian
Deerfield
Green Lake
Dodgeland
Lourdes Academy
Fall River
Markesan
Hustisford
Montello
Johnson Creek
Oakfield
Pardeeville
Princeton
Rio
Randolph
Williams Bay
Valley Christian
This alignment would only last for two years, as the Trailways split into Central, North and South Divisions in 2008:[3]
Central Division
North Division
South Division
Cambria-Friesland
Green Lake
Abundant Life Christian
Central Wisconsin Christian
Lourdes Academy
Deerfield
Markesan
Montello
Dodgeland
Pardeeville
Oakfield
Fall River
Randolph
Princeton
Hustisford
Valley Christian
Johnson Creek
Rio
Williams Bay
In 2012, Green Lake and Princeton High Schools entered into a cooperative agreement for their schools' athletics, and the newly created program remained in the North Division.[4] That same year, Horicon[5] and Madison Country Day School[6] in Waunakee joined the Trailways, and Rio moved to the North Division to keep membership at six schools. The Trailways Conference was realigned to a two-division format in 2013:
North Division
South Division
Cambria-Friesland
Abundant Life Christian
Central Wisconsin Christian
Deerfield
Green Lake/Princeton
Dodgeland
Lourdes Academy
Fall River
Markesan
Horicon
Montello
Hustisford
Oakfield
Johnson Creek
Pardeeville
Madison Country Day
Randolph
Rio
Valley Christian
Williams Bay
In 2014, Wayland Academy in Beaver Dam joined the Trailways South Division,[7] and St. Ambrose Academy in Madison joined with Abundant Life Christian School for most sponsored sports (they would move to their own stand-alone programs in 2023).[8] The North/South divisional alignment would last for two more years before the Trailways realigned to three divisions in 2016:
Central Division
North Division
South Division
Cambria-Friesland
Green Lake/Princeton
Abundant Life Christian
Central Wisconsin Christian
Lourdes Academy
Deerfield
Horicon
Markesan
Dodgeland
Pardeeville
Montello
Fall River
Randolph
Oakfield
Hustisford
Wayland Academy
Valley Christian
Johnson Creek
Madison Country Day
Rio
St. Ambrose Academy
Williams Bay
This alignment would only last a single season, as Palmyra-Eagle and Parkview joined the Trailways as all-sport members in 2017 after leaving the Rock Valley Conference,[9] bringing conference membership to the current twenty-four teams (twenty-five schools) and the current East/South/West divisional alignment.
When the Trailways Conference was formed in 2001, football was among the sports offered by the organization. Thirteen of the original fifteen members participated in the first season of competition (including the Fall River/Rio cooperative team), with Abundant Life Christian and Williams Bay being the only holdouts. ALCS did not offer football at that time, and Williams Bay was a football-only member of the Indian Trails Conference.[10] Two members who were affiliated primarily with the Six Rivers Conference (Belleville/Albany and New Glarus/Monticello) rounded out the original membership roster, and they participated in the first five seasons before their exit to join the Capitol Conference for the 2006 football season.[11] The Trailways Conference was subdivided into large-school and small-school divisions for its first season of football:
Trailways Large
Trailways Small
Belleville/Albany
Cambria-Friesland
Dodgeland
Deerfield
Fall River/Rio
Green Lake
Montello
Hustisford
New Glarus/Monticello
Johnson Creek
Pardeeville
Randolph
Princeton
Valley Christian
There were a few cooperative programs that were football participants during the conference's history due to the small size of some of its members, and divisions realigned frequently based on the acquisition of new member schools and changes in enrollment.
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.[12] In this alignment, the eight original members of the realigned Trailways Conference were Cambria-Friesland, Deerfield, Fall River/Rio, Johnson Creek, Lourdes Academy, Randolph, St John's Northwestern Military Academy and Wayland Academy.[13] Six schools were holdovers from the previous two-division setup, while St. John's Northwestern and Wayland Academy held primary affiliation in the Midwest Classic Conference. For the 2022-2023 cycle, the Trailways Conference picked up Pardeeville from the Eastern Suburban Conference as a replacement for Wayland Academy, which dropped football before returning with an eight-man football team in 2023.[14] In 2024, the Trailways Conference lost three members to the Eastern Suburban Conference (Deerfield, Fall River/Rio and Pardeeville) and St. John's Northwestern to eight-man football and the Southeast-8 Conference.[15] Dodgeland and Palmyra-Eagle moved over from the Eastern Suburban Conference and one school each moved over from the Southwest Wisconsin Activities League (Parkview/Albany) and South Central Conference (Westfield) as replacements for the four exiting members.[16] The Trailways Conference will be experiencing significant changes to football membership for the 2026-2027 cycle. Deerfield and Fall River/Rio make their return from the Eastern Suburban Conference, and Randolph will enter into a cooperative program with Cambria-Friesland. Palmyra-Eagle will be leaving the conference due to their impending transition to eight-man football and membership in the Southeast-8 Conference.[17]