The league was narrowed back to five members after Evansville downgraded football from Division I to club status in 1997. Evansville explored upgrading football again to NCAA Division I in 2007, but plans fell through. Studies still continue about a possible football resurrection, which would most likely lead to Evansville re-joining the league.
On April 8, 2005, Austin Peay announced that it would be leaving the Pioneer Football League after the 2005 season and returning to scholarship-granting competition in 2007 with the Ohio Valley Conference in which it competes in other sports. As a result, the conference was reverted to round-robin play and the divisions and championship game were removed. However, on April 7, 2006 Campbell University announced it would bring back football at the non-scholarship level for the 2008 season, and on December 5, 2007 it accepted an invitation to the PFL. In February 2008, Marist College announced that it would join the PFL for the 2009 season, after the MAAC stopped sponsoring football. Although Campbell moved in 2011 from the Atlantic Sun Conference to the Big South Conference, which sponsors football, it did not join the Big South football conference and remains in the PFL.
2013 membership changes & Automatic playoff berth
On June 13, 2011, it was announced that Mercer University and Stetson University will join the league in 2013. That will bring the league's membership to 12 schools. Starting with the 2013 season the Pioneer Football League will now have an automatic bid into the FCS division I playoffs. Before beginning play, however, Mercer announced its plans to begin offering scholarships as part of its move to the Southern Conference.
Two in-state rivalries currently exist in the PFL.
Butler and Valparaiso first played in 1927, and had nine meetings prior to 1951. That year, the two teams began playing every year, and in 2006 began playing for the Hoosier Helmet Trophy. Butler currently leads 47-24. The two schools had an all-sports rivalry as well when both were in the Horizon League together from 2007-2012.
Campbell and Davidson began their rivalry in 2008 when the Fighting Camels joined the PFL. Davidson leads 4-1.
Jacksonville and Stetson will begin their football rivalry in 2013 when Stetson begins PFL play, the schools are already rivals in other sports as both are members of the Atlantic Sun Conference.
Butler and Dayton also have a rivalry based on proximity to each other. The teams have met every year since 1977 with the exception of 1991 and 1992. Dayton leads 26-11-1.
The Pioneer Football League has had alliances with the Gridiron Classic and the Sports Network Cup. In addition, league members are allowed to accept at-large invitations to other college bowl games and teams are eligible to compete in the FCS playoffs, but can only receive at-large bids because the league is not an automatic qualifier. Until 2013, no PFL school earned an invitation to the FCS playoffs.
Starting in 2013, the Pioneer League will join ten other FCS conferences (Big Sky, Southern, Southland, MEAC, NEC, CAA, Big South, MVFC, OVC, Patriot League) that receive an automatic bid to compete in the Division I Football Championship as the playoffs expand from twenty teams to 24.
On May 16, 2006, the Pioneer Football League (PFL) and Northeast Conference (NEC) announced a four-year agreement to meet in the Gridiron Classic, an exempted postseason football game that match the champions of the two FCS football conferences.