In 1998, Florida Atlantic University announced it was pursuing the creation of an NCAAfootball program and that Howard Schnellenberger was going to lead the charge, as director of football operations and head coach. After his success in rebuilding programs at the University of Miami and the University of Louisville, Coach Schnellenberger now undertook the role of building a program from scratch. 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. Even before FAU would play an intercollegiate game, Coach Schnellenberger explained the goal of FAU football would be to play the best teams it can schedule, in order for the program to aim for a National Championship in Division I-A football. These extreme goals were not unusual from a man like Coach Schnellenberger. At Lousiville, 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.” 
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. During the August 29, 2000 first practice, dubbed the inaugural scrimmage game, FAU continued the tradition of Homecoming King, this time including the crowning ceremony of the King as part of the half time festivities. The Homecoming King crown was bestowed upon Wayne Burns, having been voted in by the majority of student population from across all the campuses at the time, which totaled five, then running a Q&A gauntlet alongside the top three candidates, conducted by a committee of students and faculty, who then voted to determine if Mr. Burns would move to the winners circle or if the next candidate would get the crown. Mr. Burns, was driven around the scrimmage game field in a convertible Rolls Royce to wave to the 164 students in the stands, many of whom voted for him. Wayne Burns was and is the oldest Homecoming King to ever receive the honor at FAU. Florida Atlantic joined the NCAA Division I-AA as an Independent team for the 2001 season. Its first-ever intercollegiate competition was against Slippery Rock University, which the Owls lost 40-7 in front of 25,632 fans at Joe Robbie Stadium.
The team finished its inaugural season at 4-6 and followed the next season at 2-9. Major accomplishments in its first two seasons include the program's first win, which came in its second game, against Bethune Cookman, 31-28, and won in the first meeting with newly created South Floridarival, Florida International University, 31-21.
On September 15, 2007 FAU defeated its first Big Ten opponent with a 42-39 victory over the University of Minnesota.  Led by Rusty Smith, FAU beat Troy University in the final game of the 2007 season to become Sun Belt Conference champions and received an invitation to the 2007 New Orleans Bowl, its first ever bowl bid. As a result, in just the seventh year of the football program's history, and the third year playing in Division I, Florida Atlantic set an NCAA record by becoming the youngest program ever to receive an invitation to a bowl game.
On August 11, 2011, Howard Schnellenberger announced he would retire at the end of the season.
On October 30, 2013, Pelini resigned from his position after admitting to school officials he was using illegal drugs, specifically marijuana and cocaine. 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 the direction of interim head coach Brian Wright. Under Pelini, the Owls compiled a 5-15 record.
Wright finished the 2012-13 season as the interim head coach, winning the team's last four games and led the Owls to its first bowl-eligible season since 2008-09.
FAU Stadium at night, first game there was October 15, 2011.
Since football's inception at FAU in 1998, Coach Schnellenberger has publicly led a campaign to build a football stadium on FAU's main campus in Boca Raton. In seven seasons of competition, the FAU Owls have called two stadiums "home" (Dolphin Stadium located in Miami Gardens and Lockhart Stadium in Fort Lauderdale, neither of which are in the same county as Boca Raton). Coach Schnellenberger argued that an on-campus stadium increases popularity of the program and attracts high-caliber recruits.
In 2006, the Florida Atlantic University Board of Trustees (FAU BoT) approved the idea of moving forward with plans to build a football stadium on Boca's campus. HKS/Schenkel Shultz are currently designing an open-air, 30,000-seat football stadium (that can eventually be expanded to 100,000 seats) and are due to report back to the FAU BoT on Sept.17th, 2007  to report projected costs and a timetable to break ground on the project.
The stadium is just a part of the university's broader concept of an "Innovation Village", covering the north end of Boca's campus. The Village will include the football stadium, a multi-use Convocation Center for volleyball, basketball and recreation, two parking garages, student housing complexes, an Alumni Center, a wellness and fitness center and strip shopping centers. The Innovation Village will be funded and constructed in stages, with the football stadium being the main concern of the first phase. All relative information on the Innovation Village can be found at FAU's Campus Master Plan (2006–2013).
Florida Atlantic wears two sets of uniforms (one for home games and one for road games). Produced and endorsed by Adidas, the uniforms are traditional in style and simple in color-schemes. The home jersey is the color of "FAU Blue" with white letters and numbers - which are outlined in "FAU Red." The chest plate sports the FAU winged logo. On the shoulder area of the jersey, the traditional, varsity three-stripes highlight the break from the shoulders to the arms. The pattern of the stripes are FAU Red- White - FAU Blue - White - FAU Red. Lastly, the arms of the jersey contain the players' numbers in white, outlined in FAU Red (not shown in picture). The road jerseys are identical in pattern of the home jerseys, simply swapping the blue body for white, and the letters and numbers combination is in FAU Blue.
The home and road pants are same in style. A white body is highlighted with a belt the color of FAU Blue. On the left side directly under the belt, "OWLS" in spelled in FAU Blue outlined in FAU Red in a traditional, varsity typeface font. The three-striped pattern which is on the jersey's shoulder section is found on the pants, as well - in the same color pattern.
Lastly, the helmet is white with the FAU winged logo on both sides. Again, the three-stripe pattern is down the middle of the helmet, in the same color pattern as the jersey and pant.
Until 2012, the Owls have worn the home uniforms at every home game and the road uniforms at every road game - there is no switching roles of the uniforms. Additionally, there is no alternate uniform for the Owls and there have not been plans for any. The uniform set is believed to be traditional and simple due to the old-fashioned, throwback style and attitude of Coach Schnellenberger.
In 2012, the Owls have introduced a new uniform design. There are owl wing patterns on the jerseys and pants which are both white or navy in color. The helmet's facemask is now white. There is also an alternate red third jersey.
On November 2, 2013, at FAU's homecoming game against Tulane University, the school unveiled a new uniform design that replaced the last names of the players with the letters FAU. This was done to show the teams solidarity amidst the illegal drug use of former head coach Carl Pelini.