[5] Stony Brook participated in the Dairy Queen Classic splitting the weekend against Kansas and host Minnesota, bringing their record to 7–5.

The Seawolves followed up beating the Yale Bulldogs three out of four in a weekend series and compiled a string of victories against Fordham and Columbia for their first five-win streak of the season.

[9] The team won two midweek non-conference games against Iona and Marist at home and then traveled to Albany for a weekend series; the Seawolves took three out of four.

[11] Stony Brook played a pair of midweek non-conference games against Fairfield and Central Connecticut, coming out victorious on both occasions and swept a four-game series at UMBC, extending their winning streak to ten games and taking command of first place in the America East with a 34–10 overall record and 12–2 conference record.

[13] Stony Brook closed the regular season with a four-game sweep at conference rival Maine to win a program record 43 games.

[14] Stony Brook earned a first-round bye in the America East tournament, hosted at Joe Nathan Field.

Needing to win three games to earn the conference title, they defeated fourth-seeded Maine 14–6 and third-seeded Binghamton 7–4 to advance to the title game, where they met up with Maine again, defeating them 13–6 to advance to the 2012 NCAA Division I baseball tournament with a 46–11 record, the best record in Division I with an .807 winning percentage.

[17][18] After losing to UCF 9–8, the Seawolves entered the loser's bracket, where they defeated Missouri State 10–7, mounting a comeback after being down four runs in the seventh inning and striking out Luke Voit with the bases loaded in the bottom of the ninth to preserve the victory.

Stony Brook put together leads in the top of the 10th and 11th innings, but LSU tied the game both times with solo home runs.

In the College World Series, Stony Brook suffered consecutive losses, falling 9–1 to UCLA and 12–2 to Florida State to end the Seawolves' Cinderella run.