When the program was restarted again in 2003, after an 18-year hiatus, Hal Mumme, formerly the head coach at the University of Kentucky, was hired as head coach. Mumme became the 12th head coach in program history and he hired Woody Widenhofer as his defensive coordinator. Upon its return, SLU decided to compete at the NCAA Division I-AA level. The team finished with a 5–7 record, the sixth-best record among start-up Division I programs since 1980. Forty-six school and/or national records were broken with freshman quarterback Martin Hankins setting 21 new standards. Before a packed house on a rainy night, Southeastern opened its first season in 18 years rallying to defeat Arkansas-Monticello, 22–17, as Hankins hit Choni Francis on a 22-yard scoring pass with 6:49 remaining in the game. Scoring the first touchdown after 18 years cemented Lions football once again. The team finished its first season 5–7 and posted a 7–4 mark in 2004. The program had a big 51–17 win over #6 McNeese State and entered the Top 25 in the national I-AA rankings. Southeastern Louisiana ranked first among NCAA Division I-AA teams in total offense per game (537.1 yards) and passing offense per game (408 yards) in 2003.
After receiving an invitation from the Southland Conference for the football program to join, the conference where the rest of SLU's sports competed, it began conference play in 2005 - where it remains a current member today.
In 2012, Ron Roberts took over as head coach for the Lions and led them to a 5–6 record. The Lions finished the season with a 5–2 record in conference play, which was the best conference record the Lions had posted in the Southland since joining in 2005. The following year, the Lions posted an 11–3 overall record. The Lions were led at quarterback by Oregon transfer Bryan Bennett. They finished with a perfect 7–0 record in conference play and earned their first-ever trip to the NCAA Division 1 playoffs. They earned a first-round bye. In the second round, the SLU faced Sam Houston State in a rematch of the regular-season game played between the two in which Southeastern won 34–21. Quarterback Bryan Bennett led a late game-winning drive to give the Lions a 30–29 thrilling victory. The Lions lost to the New Hampshire Wildcats in the quarterfinals 20–17. Bennett was first-team all-Conference in 2013. Placekicker Seth Sebastian and kickoff returner Xavier Roberson won 2013 FCS Awards from College Football Performance Awards for the top positional performances.[3]
After posting a 7–4 regular-season record in 2019 the lions earned the program's third playoff berth, hosting 10th ranked Villanova in the first round. After trailing 31–14 at halftime, Southeastern came back to upset the wildcats 45–44, led by quarterback Chason Virgil's 474 yards passing.[4]
The Cypress Mug is the turned, polished mahogany mug awarded to the winner of the Louisiana–Southeastern football game.[6]Louisiana leads the series 21–17–3 with the last game played in 2022.
