Founded in 2008, the team played in the USL Premier Development League (PDL), the fourth tier of the American Soccer Pyramid, in the Heartland Division of the Central Conference.

The team was originally part of the official development system of the Minnesota Thunder former USL First Division franchise.

They played their home games at RCTC Stadium on the campus of Rochester Community and Technical College.

The Thunder joined the PDL in 2009,[1] and played their first ever game on May 9, 2009, away at Des Moines Menace.

The Thunder lost game 2–1, with the first goal in franchise history being scored by Brian Pederson.