[1] The Storm joined the original Indoor Football League as an expansion team in 1999 as the Sioux Falls Cobras, and first took the field for the 2000 season.

In 2015, the Storm followed the Sioux Falls Stampede of the United States Hockey League to the newly constructed Denny Sanford Premier Center.

After one season in the IFL, they became members of the National Indoor Football League (NIFL) and changed their name to the Sioux Falls Storm.

Sioux Falls won its second consecutive UIF championship in 2006 at their home ground, the Arena, defeating the Lexington Horseman 72–64 on July 29, 2006.

Sioux Falls became one of the few teams in indoor football history to post a shutout, beating the Peoria Rough Riders 71–0 on June 3, 2006.

With 19 seconds left to go in the game Storm quarterback Terrance Bryant threw up a prayer, and though protested by the small crowd of Horsemen fans, it was ruled a touchdown pass.

On April 25, 2009, after switching to the Indoor Football League, the Storm were found in violation of the IFL's rule of not complying with regulations related to workers compensation coverage.

Although they tied their lowest scoring game of the season, Sioux Falls rolled over the Tri-Cities Fever 37–10 to earn the league championship after a two-year hiatus and also win its first IFL title.

[6] Sioux Falls defeated the Lehigh Valley Steelhawks 79–21 in the playoff opener, then again beat Green Bay in the semifinal and Tri-Cities (this time winning 59–32) in the United Bowl.

Bryant then retired again, as on January 6, 2014, it was announced that Dixon would be returning to the Storm, citing his desire to graduate from Augustana College and be close to his family.

Prior to the 2018 season, the Storm announced they would join Champions Indoor Football (CIF) on August 30, 2017, in order to have smaller travel budget and reignite rivalries with the nearby Sioux City Bandits and Omaha Beef.