| Year: | 2006 |
| Team: | Sioux Falls Cougars |
| Sport: | football |
| Conference: | Great Plains Athletic Conference |
| Short Conf: | GPAC |
| Record: | 14–0 |
| Conf Record: | 10–0 |
| Head Coach: | Kalen DeBoer |
| Hc Year: | 2nd |
| Off Coach: | Chuck Morrell |
| Oc Year: | 8th |
| Def Coach: | Jon Anderson |
| Dc Year: | 5th |
| Champion: | NAIA national champion GPAC champion |
| Bowl Result: | W 23–19 vs. St. Francis (IN) |
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.