| Competition: | Welsh Alliance League |
| Season: | 1999–2000 |
| Winners: | Halkyn United |
| Relegated: | Llandyrnog United |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
The 1999–2000 Welsh Alliance League was the sixteenth season of the Welsh Alliance League after its establishment in 1984. The league was won by Halkyn United.