The 1999–2000 Northern Football League season was the 102nd in the history of Northern Football League, a football competition in England.[1]
| Competition: | Northern Football League Division One |
| Season: | 1999–2000 |
| Winners: | Bedlington Terriers |
| Relegated: | Thornaby-On-Tees Shotton Comrades South Shields |
| Matches: | 380 |
| Total Goals: | 1174 |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
Division One featured 17 clubs which competed in the division last season, along with three new clubs, promoted from Division Two:
Also, Stockton changed name to Thornaby-On-Tees.
| Competition: | Northern Football League Division Two |
| Season: | 1999–2000 |
| Winners: | Brandon United |
| Promoted: | Brandon United Newcastle Blue Star Hebburn |
| Matches: | 342 |
| Total Goals: | 1218 |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
Division Two featured 16 clubs which competed in the division last season, along with three new clubs, relegated from Division One:
Also, Ryhope CA changed name to Kennek Ryhope CA, while Washington changed name to Washington Ikeda Hoover.