The franchise was founded in 2009 as the New York Aviators and began play in the former North East Professional Hockey League. After the completion of the 2009-10 NEPHL season, the Aviators moved to the newly formed Federal Hockey League. The Aviators recorded a 21-game winning streak during the first season in the FHL and finished first place in the 2010-11 FHL regular season.
In the 2010-2011 Playoffs, the Aviators advanced to the Championship Series where they lost in game four to the Akwesasne Warriors of Ontario.
The team was renamed Brooklyn Aviators for the 2011-2012 season.
During the 2011-2012 Playoffs, the Aviators lost an amazing best-of-three series in the first round to the Danbury Whalers. The Aviators hosted game 1 as the 4 seed and were trailing 3-0 headed into the 3rd period. Scoring 4 unanswered goals, the Aviators held a 4-3 lead until 3 seconds remained where the Whalers scored a disputable goal. The net was not lined with the crease and play should have been whistled dead. The Aviators eventually lost Game 1 in Overtime. The series shifted to Danbury, the 3 seed, for the final two games. he Aviators won Game 2 on the road in Danbury with a commanding victory. In another exciting yet heartbreaking game for Aviator fans, the Aviators lost 5-4 in Sudden-Death Overtime to the Whalers who would eventually lose in the Championship series to the New Jersey Outlaws.
The Aviators have ceased operations and will not return for the 2012-13 season.