The club was founded by Amadu Meyers in 2016, coinciding with the announcement that it would be joining NPSL as an expansion team for the 2017 season.

[4] The club played their inaugural match on May 13, 2017 at Yankton Trail Park in Sioux Falls against the Dakota Fusion FC.

The first goal scored in team history came in the 6th minute when Houston Hoffman connected on a penalty kick.

After the regular season concluded Nigel Nielsen, Thunder midfielder, was named to the North Conference XI team.

[6] Bold Signifies a Current Thunder Player Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.