In 1997, the league reduced to five members when the University of Evansville downgraded football from Division I to club status; Evansville explored upgrading football back to Division I in 2007, but decided against it.
On April 8, 2005, Austin Peay announced its departure from the league effective after the 2005 season; Austin Peay returned to scholarship-granting competition in 2007 as a member of the Ohio Valley Conference in which it competes in other sports. As a result, the conference reverted to round-robin play; the divisions and championship game were abolished. On April 7, 2006, Campbell University announced the reinstatement of football effective in 2008, and on December 5, 2007, 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 in football and remains in the PFL.
2013 membership changes & automatic playoff berth
On June 13, 2011, Mercer University and Stetson University were announced as league members (effective 2013) bringing membership to 12 schools. In addition, as of 2013, the league has an automatic bid into the FCS division I playoffs. Soon after its PFL membership was announced, Mercer accepted an invitation to join the Southern Conference (scholarship-granting) effective July 1, 2014. During its one season in the league, Mercer set a Division I win-loss record for start-up programs; Mercer finished the 2013 season with an overall record of 10-2 including an undefeated 8-0 record at home, also a Division I record held jointly with Auburn University, which likewise went undefeated at home in 2013.
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.