| Competition: | ntfl |
| Year: | 1999–2000 |
| Teams: | 7 |
| Premiers: | Waratah |
| Count: | 15 |
| Minor Premiers: | Waratah |
| Wooden Spooners: | Wanderers |
| Wscount: | 25 |
| Prevseason: | 1998 |
| Nextseason: | 2000 |
The 1999–2000 NTFL season was the 79th season of the Northern Territory Football League (NTFL).[1]
Waratah have won there 15th premiership title while defeating the Palmerston Magpies in the grand final by 40 points.