The team began play in 2009 with a planned full transition to the NCAA Football Bowl Subdivision (Division I-A) by 2013.

[1] On September 5, 2009, the University of South Alabama Jaguars defeated Hargrave Military Academy 30–13 in the program's first ever game in front of more than 26,000 fans.

The 2011 season marked the beginning of South Alabama's two-year transition phase from unclassified to Division I FBS status.

The 2012 season was South Alabama's final year in the transition phase to full Division I-FBS status.

The South Alabama Jaguars gained full Division I FBS status for the 2013–14 season in the Sun Belt Conference.

The South Alabama Jaguars finished the 2014 season with a record of 6–6,[8] making them bowl eligible for the second straight year.

On December 3, President Tony Waldrop, on behalf of the university and the football team, accepted an invitation to play in the inaugural Raycom Media Camellia Bowl.

[11] In 2016, South Alabama recorded its first victory over an SEC opponent when it defeated Mississippi State by a score of 21–20 the opening weekend of the season.

He was fired by the university at the end of the 2020 season after a 29–0 loss to rival Troy and finished with a 9–26 record in his time with the Jaguars.

In his second season as the head coach, Wommack led the team to a 10–2 record (7-1 in conference play) and their first bowl game since the Joey Jones era.

In his third season as the head coach, Wommack led the team to a 7–6 record (4–4 in conference play) and their first bowl game win in program history.

Opened in 1948, the first event held inside the stadium was a college football game between the Alabama Crimson Tide and the Vanderbilt Commodores on October 2, 1948.

Ladd–Peebles has hosted various other events, from concerts and boxing matches to festivals, and has a present full-capacity of 40,000 (per Ladd Peebles stadium) seats.

[21] The South Alabama Football Fieldhouse covers 49,000 square feet of space, which includes an 8,000-square-foot weight room.

An attempt by the students of the university to entice a grassroots movement for support of NCAA football in 2006 led to multiple acts of temporary and non destructive vandalism across the campus organized in a single night dubbed by the organizing students as "viva la resistance".

Since the Jaguar football team was established homecoming has featured an event called "junk the jungle", in which toilet paper and streamers are used to cover all the trees in the school's central traffic circle.

The individual pranks were conducted by small teams where the final act of "junking the jungle", included all the students invited to participate.