The 2006 Sioux Falls Cougars football team represented the University of Sioux Falls in the 2006 NAIA football season.
The Cougars won the 2006 NAIA Football National Championship with a 23–19 victory over the top-ranked St. Francis Cougars.
The team also won the Great Plains Athletic Conference championship with a perfect 10–0 record.
This was the school's second NAIA Championship (1996).
The team was coached by Kalen DeBoer.