In 1999, New York Mayor Rudolph Giuliani announced a deal that would bring two minor league baseball teams to the boroughs outside Manhattan.

The Cyclones managed by Edgar Alfonzo played well in their opening season with the best record in the league (52–24), where they led the NY Penn-League with a 2.35 team ERA.

The deciding game won by the Cyclones 4–1 featured trickery by Catcher Brett Kay who faked giving up on a play only to receive a laser throw from John Toner to tag out a runner at the plate.

In 2003, the Cyclones managed by Tim Teufel won the McNamara division title with brilliant pitching led by starters, soon to be major leaguers, Matt Lindstrom and Brian Bannister and by relievers Robert Paulk and Carlos Muñiz.

With the series tied, the Cyclones were leading 3–0 in the 3rd inning when the games was held up and eventually cancelled by rain, which wiped out the score.

On August 23, 2005, The Cyclones and KeySpan Park hosted the first-ever New York–Penn League All-Star Game, which was won by the National League–affiliated team.

Cyclones manager George Greer was ejected from the contest in the first inning for arguing an umpire's call on a force play at second base.

With a consistent offense, great pitching and the best defense in the league, the Cyclones powered their way to winning its fourth McNamara division title and sweeping the SI Yankees in two straight games in the NYPL opening playoff round.

After giving up a leadoff home run to shortstop Matt Bouchard, future Toronto Blue Jays starting pitcher Brett Cecil pitched one hit ball in 7 innings as the Doubledays won the game 4–1.

On September 7, 2007, during the final regular season game (a 5–4 victory over the Lowell Spinners), the Cyclones set an all-time single-game attendance record of 10,073—2,573 more than the stadium's seating capacity in 2001.

The team produced major leaguers and future New York Mets Ike Davis and Jenrry Mejía.

On August 23, 2009, Cyclones pitcher Brandon Moore threw a 7-inning no-hitter in the first game of a doubleheader against the Aberdeen IronBirds, 5–0, at Ripken Stadium.

This came seven years to the day Miguel Pinango threw a nine-inning one-hitter for the Cyclones, pitching 8+2⁄3 innings of no-hit ball.

Since 2014, the Cyclones have dedicated one night a year as a tribute to the popular sitcom Seinfeld, featuring various show tributes such as an "Elaine Benes dancing contest", determining if a fan had either picked or scratched their nose, the Cyclones wearing "Puffy Shirt"–styled jerseys, appearances from former actors and giveaways honoring the show.

This game has since become one of the Cyclones' most popular events, regularly selling out in advance and drawing fans of both baseball and Seinfeld from near and far.

The Brooklyn Cyclones returned to the New York-Penn League playoffs in 2019, thanks to a strong finish to end the season, which included a series sweep of the Staten Island Yankees in what would be the final match-up between the longtime rivals.

The Cyclones took Game 2 in Brooklyn by a score of 1–0, thanks to a solo homer from Jed Lowrie, who was on a rehab assignment from the Mets.

After a solo homer by Marino Campana in the Top of the 7th put Lowell up 3–2, the Cyclones staged a rally to take a 4–3 lead, en route to winning the 2019 New York-Penn League Championship.

This has led to a unique situation, as the longtime Vice President of the Brooklyn Cyclones is also named Steve Cohen, but unrelated to the new owner.

A major contribution to this intense rivalry was the fact that both parent teams were also based in New York (the Mets in Queens, and the Yankees in the Bronx).

[6] In 2022, the High-A East became known as the South Atlantic League, the name historically used by the regional circuit prior to the 2021 reorganization.

[1] The first Cyclone to break into the major leagues was infielder Danny Garcia, who made his debut with the New York Mets on September 2, 2003, at Shea Stadium.

Scott Kazmir, who played with Brooklyn in 2002, made his major league debut with the Tampa Bay Devil Rays in 2004.

Mike Jacobs, who was a member of the inaugural 2001 Cyclones team, made his Mets debut on August 21, 2005, hitting a three-run pinch-hit home run off Washington Nationals pitcher Esteban Loaiza.

In 30 games with 100 at bats for the Mets, Jacobs hit 11 home runs and had 23 RBI before being traded to the Florida Marlins after the season.

In April 2006, Brian Bannister became the first Cyclone pitcher to make his debut with the Mets in a game against the Washington Nationals at Shea.

The following April, sidearm reliever Joe Smith, who pitched for the Cyclones in 2006, made his major league debut on opening day for the Mets against the St. Louis Cardinals.

Brooklyn Dodgers: 4: Duke Snider; 14: Joan and Gil Hodges 17: Carl Erskine; 36: Don Newcombe; 42: Jackie Robinson; Brooklyn Cyclones: 6: Danny Garcia; 19: Brian Bannister; 20: Dillon Gee; 35: Ángel Pagán; NOTE: A Cyclones player may still wear these numbers, with the exception of 14, and 42.

On August 22, 2011, the Brooklyn Cyclones also honored Pia Toscano, who sang the anthem prior to a game in 2003 by putting a plaque on the press level.

August 2010 – 2021: Mark Fratto, who also serves as the PA Announcer for NYCFC, the Washington Wizards, the Westchester Knicks and Sky Blue FC.