The 1998–99 Northern Football League season was the 101st in the history of Northern Football League, a football competition in England.[1] Division One was won by Bedlington Terriers and Division Two was won by Durham City. Bedlington opted against promotion to the Northern Premier League.
The league held two cup competitions. The Northern League Cup, competed for by all Northern League sides, was won by Dunston Federation. They beat Jarrow Roofing 4–1 in the final. The Craven Cup, for Division Two teams, was won by Ashington defeating Evenwood Town 1–0 in the final.
| Competition: | Northern Football League Division One |
| Season: | 1998–99 |
| Winners: | Bedlington Terriers |
| Relegated: | Newcastle Blue Star Penrith Shildon |
| Matches: | 380 |
| Total Goals: | 1332 |
| Prevseason: | 1997–98 |
| Nextseason: | 1999–2000 |
Division One featured 17 clubs which competed in the division last season, along with three new clubs, promoted from Division Two:
Also, RTM Newcastle changed name to Newcastle Blue Star.
| Competition: | Northern Football League Division Two |
| Season: | 1998–99 |
| Winners: | Durham City |
| Promoted: | Durham City Shotton Comrades Peterlee Newtown |
| Matches: | 342 |
| Total Goals: | 1211 |
| Prevseason: | 1997–98 |
| Nextseason: | 1999–2000 |
Division Two featured 16 clubs which competed in the division last season, along with three new clubs, relegated from Division One:
For Division Two teams