| Year: | 1999 |
| Team: | Northern Illinois Huskies |
| Sport: | football |
| Conference: | Mid-American Conference |
| Division: | West Division |
| Short Conf: | MAC |
| Record: | 5–6 |
| Conf Record: | 5–3 |
| Head Coach: | Joe Novak |
| Hc Year: | 4th |
| Off Coach: | Dan Roushar |
| Oc Year: | 2nd as OC; 3rd overall |
| Mvp: | William Andrews, Donnavan Carter |
| Captain: | Donnavan Carter, Ryan Diem, Chris Finlen, Lamain Rucker, Mike Stack |
| Stadium: | Huskie Stadium |
The 1999 Northern Illinois Huskies football team represented Northern Illinois University as a member of the West Division of the Mid-American Conference (MAC) during the 1999 NCAA Division I-A football season. Led by fourth-year head coach Joe Novak, the Huskies compiled an overall record of 5–6 with a mark of 5–3 in conference play, tying for second place in the MAC's West Division. Northern Illinois played home games at Huskie Stadium in DeKalb, Illinois.