After a year of FCS independence, Stony Brook joined the Big South Conference and fully transitioned into a 63-scholarship program.

[8] After Stony Brook University's growth saw its enrollment rise to over 16,000 students, the athletic department started taking shape with the steady development of its collegiate programs.

Football was one of them, and Stony Brook initiated competition against regional universities and fellow SUNY members schools.

The Liberty Football Conference was a New York-only league where Stony Brook played again teams such as Hofstra, St. John's and Iona.

[14] Stony Brook transitioned into a scholarship team with full funding beginning in 2006 and Chuck Priore was named the Seawolves' second head coach in program history.

[15][16][17][18] In Priore's first season, Stony Brook awarded the equivalent of 27 scholarships to 38 players and began broadcasting its games on 90.1 WUSB-FM, the campus radio station.

[30] In 2009, Stony Brook won its first share of the Big South title by winning five of six conference games, including upsetting Liberty 36–33 in the season finale.

[32] Hofstra running back duo Miguel Maysonet and Brock Jackolski both transferred to Stony Brook in the offseason.

[33] The 2010 season saw Stony Brook schedule its first game against an FBS opponent, losing 59–14 to South Florida despite leading for the entire first quarter.

[34] While Stony Brook won its first five conference games by at least two scores, they lost 54–28 to Liberty in the season finale, settling for a share of its second straight share of the Big South title but not the automatic bid to the FCS Playoffs, which Coastal Carolina won by allowing the least points in conference play.

[35]Stony Brook lost its first two games in 2011 to FBS teams, falling to UTEP 31–24 in overtime after allowing 21 unanswered points and being routed 35–7 by Buffalo.

[38] Then, Stony Brook began a program-record nine-game winning streak, beating Lafayette 37–20 in the conference opener and scoring at least 40 points in each game for the rest of the regular season.

[39] In the first round of the 2011 FCS Playoffs, Stony Brook paired up against in-state rivals Albany, coming back from an 18-point deficit to defeat the Great Danes 31–28 in front of a then-record-setting crowd of 8,286, capped off by a game-sealing interception from safety Dominick Reyes.

[40] In the second round, Stony Brook lost 34–27 to top-seeded Sam Houston State to end the season at 9–4 (6–0 Big South).

[41] Before the 2012 season, the Seawolves added several FBS transfers, including Iowa's Marcus Coker, Maryland's Adrian Coxson, and Minnesota's Leston Simpson.

Stony Brook lost the season finale 28–14 to Liberty, giving Coastal Carolina the autobid, but won a share of the Big South title for the fourth straight year.

[51] Maysonet ran for 1,964 yards and 23 touchdowns in 2012 but finished in second place behind Old Dominion quarterback Taylor Heinicke for the Walter Payton Award, given to the top FCS player in the country.

[58] The 2014 season began with losses to non-conference opponents Bryant and FBS UConn, and Stony Brook's record stood at 1–4 by the end of September.

[59] Stony Brook began their 2015 season with a match against FBS Toledo, but the game was suspended and canceled due to severe thunderstorms.

19 FBS-ranked South Florida, Stony Brook ended the season with a 10–3 record, going 7–1 in CAA play to finish in second place behind James Madison.

[70] In the regular season finale, Stony Brook won 20–19 at Maine on a Hail Mary which was caught in the end zone as time expired in the fourth quarter; the pass was ranked No.

10 Stony Brook was massively upset on the road, losing 25–23 to last-place Albany in a rivalry game that was decided on a last-second field goal.

[80] Regardless, Stony Brook still earned an at-large berth to the FCS Playoffs after finishing 7–4 (5–3 CAA), where they lost 28–14 to Southeast Missouri State in the first round.

[81] Stony Brook began 2019 with a 4–1 record, losing only to FBS Utah State and future first-round NFL quarterback Jordan Love.

[84] The 2020 season was played in spring 2021 due to the COVID-19 pandemic, where Stony Brook went 1–3 against all CAA teams and saw its final two games canceled because of opponents' outbreaks.

[89] In 2022, Stony Brook finished with a program-worst 2–9 record, but managed to outdo themselves in futility in 2023 by going 0–10 for the first winless season in program history.

In 2009, the Seawolves were named co-conference champions of the Big South Conference after finishing 6–5 (5–0) but did not earn a bid to the FCS Playoffs.

[92] Albany, Stony Brook's in-state rival, first played the Seawolves in 1995 when both programs were at the Division II level.

In October 2012, it was reported that the University has allocated $5.7 million for the addition of at least 2,000 seats to LaValle Stadium, which would bring the capacity up to 10,300.

In February 2011 it was announced that a new strength and conditioning center will be erected in the north side of the Stony Brook indoor Sports Complex.