Schnellenberger was a former offensive coordinator with the NFL's Indianapolis Colts and Miami Dolphins who, as a head coach, turned around a moribund Miami football program and won a national championship in his fifth season in 1983 after back to back nine win seasons in 1980 and 1981.

Much like his time at Miami and Louisville, Coach Schnellenberger did not shy from placing lofty expectations and high goals on his newly created program.

At Louisville, facing threats from the administration that the football team would be terminated, Schnellenberger made the bold (and now famous) prediction, "[We are] on a collision course with the national championship.

The only variable is time.”[2] On August 29, 2000, the first practice was held at the Boca Raton campus of FAU, and 164 students showed up to try out for the team.

[6] On December 1, 2011, FAU hired Carl Pelini, the Nebraska Cornhuskers defensive coordinator to become their new head coach, to succeed Schnellenberger.

[7][8] He, along with defensive coordinator Pete Rekstis, officially stepped down from their positions only three days before the school's homecoming game, which they won 34–17 under interim head coach Brian Wright.

[13] Kiffin resigned from FAU on December 7, 2019, after a 49–6 blowout win against the university of Alabama at Birmingham (UAB) and before FAU's Boca Raton Bowl appearance against SMU Mustangs to become the head coach at the University of Mississippi (Ole Miss).

[15][16] FAU's first year defensive coordinator, Glenn Spencer, was named the interim head coach to lead the Owls at the Boca Raton Bowl.

[18] During a shortened season due to the COVID-19 pandemic with no prior spring practice, Taggart led the FAU Owls to a 5–4 record, which includes a loss to the Memphis Tigers in the first and only Montgomery Bowl.

Zach Kittley, former offensive coordinator at Houston Baptist, Western Kentucky, and Texas Tech, was hired as the next coach at FAU on December 2, 2024.

† Co-champions ‡ 2019 Boca Raton Bowl win coached by Glenn Spencer As a member of Conference USA since 2013, Florida Atlantic competes in the East Division.

In total the two squads have met 21 times with Florida Atlantic holding a 16–5 lead as of the 2023 season conclusion.