| Year: | 1999 |
| Team: | Southern Jaguars |
| Sport: | football |
| Conference: | Southwestern Athletic Conference |
| Division: | West Division |
| Short Conf: | SWAC |
| Record: | 11–2 |
| Conf Record: | 4–0 |
| Head Coach: | Pete Richardson |
| Hc Year: | 7th |
| Stadium: | A. W. Mumford Stadium |
| Champion: | SWAC champion SWAC West Division champion |
| Conf Champ: | SWAC Championship Game |
| Conf Champ Result: | W 31–30 vs. Jackson State |
| Bowl: | Heritage Bowl |
| Bowl Result: | L 3–24 vs. Hampton |
The 1999 Southern Jaguars football team represented Southern University as a member of the Southwestern Athletic Conference (SWAC) during the 1997 NCAA Division I-AA football season. Led by seventh-year head coach Pete Richardson, the Jaguars compiled an overall record of 11–2, with a conference record of 4–0, and finished as SWAC champion.