* = forfeit Early in 2003, the APFL started as a regional league with the Kansas Koyotes, Missouri Minutemen, St. Joseph Explorers, and Chillicothe Lumberjacks.

However, the Lumberjacks didn't make it to opening day and as a result the league played on with three teams while Chillicothe was replaced on the schedule.

Jerry Lakin hit a game-winning field goal and Kansas completed their third consecutive undefeated season with a 26–24 win.

The Kansas Storm attempted to move to St. Joseph, Missouri but ended up not playing in 2006, causing the league to find replacements for their games on the schedule.

After Kansas won their semi-final against the Blackhawks, the league decided to move the championship game to Landon Arena, home of the Koyotes.

The MAIFL champion Springfield Wolfpack and two new teams from Texas, the Conroe Storm and Fort Worth Regulators, joined the league for the 2007 season.

The Wichita Falls Diablos and former NIFL members Beaumont Drillers and Florida Scorpions joined Conroe and Fort Worth in the Southern Division.

Arena problems and mismanagement plagued many teams throughout the league, resulting in a cancellation of the entire season for Ft. Worth.

The Scorpions continued to play in the league as a travel-only team, as did the renamed Nebraska Tornadoes and new member Denver Titans.

Junction City joined as a travel-only team and primarily played in the Central Plains Football League.

The Outlaws came to the league after winning the CPFL title three years in a row and were also notable for defeating the Blackhawks in a matchup during the 2009 season.

In February 2011 the league added the Florida Scorpions and Kansas City Matadors as provisional members to fill out their 2011 schedule.

After the 2012 season, several teams left to start the Champions Professional Indoor Football League, including the Kansas Koyotes, which was sold off.

In 2015, the Crunch became one of four teams to join the North American Indoor Football League for its inaugural season.