The Capitol Conference was formed in 1969 after the breakup of the larger Madison Suburban Conference into three separate organizations. Six of its original members came from the conference's Western section (Lodi, McFarland, Poynette, Verona, Waunakee and Wisconsin Heights) and two came from the Central section (DeForest and Waterloo). In 1977, Poynette left to rejoin the Dual County Conference (having previously been a member from 1926 to 1954) and Waterloo became a member of the Eastern Suburban Conference. Two schools moved over from the Central Suburban Conference (Columbus and Lake Mills) to take their place and keep the conference at eight member schools. Mount Horeb joined the Capitol Conference after leaving the Southern Eight Conference in 1983, replacing Lake Mills, who briefly joined the Eastern Suburban Conference. In 1987, DeForest and Waunakee left to become the newest members of the Badger Conference with Lake Mills and Poynette rejoining the Capitol Conference as their replacements.
1994-2006
By 1994, the Verona Area School District was the fastest-growing district in the Madison area, and they were invited to enter the Badger Conference with an eye towards continued future growth. Lakeside Lutheran in Lake Mills took their place in 1995 after leaving the Eastern Suburban Conference, renewing their crosstown rivalry with Lake Mills. Cambridge, Marshall and Waterloo followed Lakeside Lutheran out of the Eastern Suburban in 2001, offsetting the loss of Lodi and Poynette to the South Central Conference and McFarland and Mount Horeb to the Badger Conference. For Waterloo, this was their second stint in the conference after having been a member from 1969 to 1977. The Capitol Conference would remain a seven-member league for the next five years before major changes would occur.
2006-present
In 2006, the Capitol Conference reached its high of twelve member schools when Lodi and Poynette rejoined from the South Central Conference, Belleville and New Glarus came over from the Six Rivers Conference and Luther Prep in Watertown was added after being displaced from the Parkland Conference when it ceased operations. With the addition of the new schools came realignment into the Capitol North and Capitol South divisions:
Capitol North
Capitol South
Columbus
Belleville
Lake Mills
Cambridge
Lakeside Lutheran
Marshall
Lodi
New Glarus
Luther Prep
Waterloo
Poynette
Wisconsin Heights
This alignment stayed intact for sixteen years before Luther Prep exited the conference to rejoin the Midwest Classic Conference in 2023. In 2025, Waupun joined from the disbanded East Central Conference, taking Luther Prep's place in the Capitol North. For the 2027-28 school year, the WIAA's Board of Controls approved a move by Portage from the Badger Conference Small Schools division to the Capitol Conference as its thirteenth member.
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. Eight schools were designated as football members for the Capitol Conference: Big Foot, Columbus, Horicon/Hustisford, Lake Mills, Lakeside Lutheran, Lodi, Luther Prep and Turner. The Capitol Conference also operates a small-school division consisting of Cambridge, Clinton, Dodgeland, Markesan, Marshall, Palmyra-Eagle, Pardeeville and Waterloo. This conference competes under the Eastern Suburban Conference banner, which was the name of an all-sport conference that last played in 2001. Several schools entering the Capitol Conference for football had primary affiliations with the Rock Valley and Trailways Conferences. In 2022, Horicon/Hustisford moved over to the Eastern Suburban Conference and Luther Prep left to join the Midwest Classic Conference. The six remaining schools in the Capitol Conference welcomed Edgewood from the Rock Valley Cofnerence and New Glarus/Monticello from the Southwest Wisconsin Conference to bring the roster to eight schools. Three schools left the Capitol Conference football alignment in 2024: Edgewood and Lakeside Lutheran left the Capitol Conference as football members in 2024 to join the Badger Conference, and New Glarus returned to the Southwest Wisconsin Conference after a two-year absence. The two outgoing schools were replaced by Clinton and Horicon/Hustisford, with the latter making their return from the Eastern Suburban Conference. The Capitol Conference will be receiving a massive overhaul to their football roster for the 2026-27 cycle, losing former associate members Big Foot, Clinton and Turner to full affiliation with the Rock Valley Conference and Horicon/Hustisford to a return to the Eastern Suburban Conference. They will be replaced by former Badger Conference members Lakeside Lutheran and Portage and two schools from the Rock Valley Conference (Edgerton and Jefferson). The conference will also be gaining a scheduling partner in the Rock Valley, with one mandatory crossover game per season counting towards conference standings.
