The team plays its home games at Island Federal Credit Union Arena, located on the university's campus in Stony Brook, New York.

[7] Coaches Ron Bash, Dick Kendall, and Joe Castiglie helped develop the program in the late 1970s and 1980s, and by the early 1990s, Stony Brook participated in the New York metropolitan-based Skyline Conference.

The transition period occurred from 1995 to 1999, when head coach Bernard Tomlin led Stony Brook at the Division II level.

[11] On June 10, 1999, Tomlin was reassigned and Stony Brook hired Fordham head coach Nick Macarchuk to begin its tenure in Division I.

[15][16] Steve Pikiell, a former UConn point guard and recently the associate head coach at George Washington, was hired on April 13, 2005.

The NCAA Committee of Infractions discovered that 53 athletes in 14 sports from 1999 to 2001 were ineligible to compete due to improper paperwork and lack of academic credit hours.

[18] Stony Brook finished in last place during Pikiell's first season with a 4–24 (2–14 AE) record, but his first recruiting class was named 32nd-best in the nation and he was extended through 2010–11 on March 23, 2006.

1 seed in the America East tournament, the Seawolves beat eighth-seeded Albany 68–59 in the quarterfinals but lost to Boston University 70–63 in the semifinals.

[25] The successful season led to the school's largest broadcasting package, with three games scheduled on the main ESPN channel, two on ESPNU, one on SNY and five on MSG+.

With the score tied at 54 with 2.4 seconds left, Holland was fouled and made both free throws as Stony Brook lost 56–54 and their first NCAA tournament bid came up short.

[34] Stony Brook earned its second America East regular season championship and won 14 games in conference for the first time, one of 13 Division I teams to go undefeated at home.

Stony Brook won a second straight regular season title, winning 14 of its last 16 games to enter the postseason.

1 seed, Stony Brook beat Binghamton 72–49 in the America East quarterfinals[41] but was upset by fourth-seed Albany in the semifinals.

Playing against Albany in front of a sold-out crowd at Pritchard Gymnasium, the Seawolves led 52–46 with 7:02 remaining, but the Great Danes roared back and defeated Stony Brook 69–60.

As a sophomore, Warney won his first America East Player of the Year after ranking top five nationally in field goal percentage and leading Stony Brook in scoring, rebounding, and blocking.

[55] Stony Brook beat Binghamton and Vermont to reach its fourth America East finals in five years, still searching for their first NCAA tournament berth.

Stony Brook beat UMBC 86–76 in the quarterfinals and Hartford 80–64 in the semifinals, making their third straight America East Finals and their fifth in six years.

[66] Warney won his third consecutive America East Player of the Year award, averaging a double-double for the second straight season.

[67] On March 20, 2016, three days after Stony Brook's NCAA tournament appearance, Pikiell accepted the head coaching job at Rutgers, ending his Seawolves tenure with a 192–157 record in 11 seasons.

[70] Stony Brook beat Binghamton 70–60 in the America East quarterfinals but was upset at home by three-seed Albany in the semifinals, 63–56.

[76] Stony Brook began the 2018–19 season by beating George Washington 77–74 in overtime after trailing 22–0, the largest scoreless comeback in college since 1977.

[81] On March 17, 2019, Boals resigned to accept the head coaching job for the Ohio Bobcats, his alma mater, going 55–41 overall and 33–17 in the America East in three seasons.

[82] Geno Ford was promoted from assistant to interim head coach for the 2019 College Basketball Invitational, where the Seawolves blew a 25-point first-half lead against South Florida, ultimately losing 82–79 in overtime.

[83] On March 26, 2019, Ford's interim tag was removed and he was officially named the fourth head coach in the program's Division I era.

[85] After defeating Albany in the America East quarterfinals, Stony Brook was upset 64–58 at home by Hartford in the semifinals to end their season at 20–13.

Stony Brook earned a CAA tournament win over North Carolina A&T, 76–61 in the first round, losing to champions Charleston in the quarterfinals.

Seeded seventh in the CAA tournament, Stony Brook earned upsets over two-seed Drexel, 91–88 (2OT) in the quarterfinals,[96] and three-seed Hofstra, 63–58 in the semifinals[97] to face top-seed Charleston in the championship game.

Up by five at halftime, Stony Brook scored the final nine points in regulation to force overtime but lost 82–79, one win shy of an NCAA tournament bid.

The campus was originally located in Oyster Bay, New York when the school was known as the State University College on Long Island, moving to Stony Brook in 1962.

Warney, a three-time America East Player of the Year, is Stony Brook's all-time leader in career points, rebounds, blocks, and games played.