It is operated by the Federal Bureau of Prisons, a division of the United States Department of Justice.

[1] The site, located 75 miles (121 km) from Minneapolis, was converted into a prison in 1992 after formerly serving as a University of Minnesota campus.

In 2006, FCI Waseca received its most high-profile prisoner when Jeffrey Skilling, CEO of the now defunct Enron Corporation was sent there after he was convicted of insider trading, securities fraud and other charges for making a $60 million profit by selling company stock in anticipation of the company's 2001 collapse.

The FBI was called in to investigate an act of violence at FCI Waseca in June 2011.

Thomas pleaded guilty to assault with a dangerous weapon on January 11, 2013 and was subsequently sentenced to an additional 41 months in prison.