Stony Brook currently competes in the Coastal Athletic Association (CAA) and plays its home games on Joe Nathan Field.

He debuted for the Giants in 1999 as a pitcher, becoming the first player in program history to play in the MLB.Stony Brook began in Division I as a member of the Eastern College Athletic Conference.

In 2003, Stony Brook advanced to its first America East Tournament title game, needing to beat Northeastern twice to win the championship.

[6] Stony Brook was assigned as the fourth seed in the Kinston Regional, where they lost to host East Carolina 8–2 and Tennessee 1–0 and were eliminated from the tournament in two games.

Stony Brook was ousted early in the America East tournament after consecutive losses against second-seeded Albany and fourth-seeded Vermont.

[16] Stony Brook won its first conference regular season title in 2011 after going 22–2 in America East play; the Seawolves ended with a program-record 42 wins and went 42–12.

However, Stony Brook was upset twice in the America East Tournament, once by Albany and again by Maine to eliminate the Seawolves before reaching the title game, putting their record-breaking season to a stunning halt.

The Seawolves continued to earn non-conference wins against Iona, Marist, Rhode Island, Central Connecticut and Fairfield in the middle of the conference season, entering the America East tournament with a 43–11 record.

Following a loss to second-seeded Central Florida, Stony Brook beat Missouri State in dramatic fashion, striking out Luke Voit in the bottom of the ninth with the bases loaded in a 10–7 win.

[25] In a rain-soaked Baton Rouge Super Regional, Stony Brook fell in the first game to LSU, who started pitcher Aaron Nola, in an extra-innings affair that spanned two days due to rain.

[28] In the College World Series, Stony Brook's Cinderella run came to an end, losing to UCLA 9–1 and Florida State 12–2.

[31] Stony Brook followed up its College World Series campaign with a disappointing 25–34 season, finishing fourth in the America East and being eliminated in the first two games of the tournament.

[34] Playing in the Fort Worth Regional, the Seawolves lost to North Carolina State 3–0, beat Sacred Heart 11–6 and were eliminated with an 8–3 loss to TCU.

[35] In 2016, Stony Brook finished in third place in the America East, advancing to the tournament championship from the loser's bracket before falling to Binghamton.

[37] Stony Brook finished in fourth place in 2018, again reaching the championship game from the loser's bracket and losing to Hartford.

[39] In the NCAA tournament, Stony Brook was placed in the Baton Rouge Regional, scheduled to face LSU in a rematch of the 2012 series that sent the Seawolves to Omaha.

[40] The Seawolves were eliminated from the NCAA tournament with a following 13–5 loss to Arizona State, which rostered future number-one MLB draft pick Spencer Torkelson.