The 1999–2000 Hellenic Football League season was the 47th in the history of the Hellenic Football League, a football competition in England.
At the end of the season the Hellenic League merged with the Chiltonian League. 17 clubs from the latter formed Division One East, while Hellenic League Division One clubs formed Division One West.
| Competition: | Hellenic Football League Premier Division |
| Season: | 1999–2000 |
| Winners: | Banbury United |
| Promoted: | Banbury United |
| Matches: | 342 |
| Total Goals: | 1091 |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
The Premier Division featured 16 clubs which competed in the division last season, along with three new clubs:
| Competition: | Hellenic Football League Division One |
| Season: | 1999–2000 |
| Winners: | Cheltenham Saracens |
| Promoted: | Cheltenham Saracens Wootton Bassett Town |
| Matches: | 210 |
| Total Goals: | 684 |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
Division One featured 13 clubs which competed in Division One last season, along with two new clubs, joined from the Oxfordshire Senior League: