The 1999–2000 season was the 58th in the history of Eastern Counties Football League a football competition in England.[1]
Histon were champions, winning their first Eastern Counties Football League title and were promoted to the Southern Football League for the first time in their history.
| Competition: | Eastern Counties Football League Premier Division |
| Season: | 1999–2000 |
| Winners: | Histon |
| Promoted: | Histon |
| Matches: | 420 |
| Total Goals: | 1303 |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
The Premier Division featured 20 clubs which competed in the division last season, along with two new clubs, promoted from Division One:
Sudbury Town merged with Sudbury Wanderers to form new club AFC Sudbury.
Histon won the league on the last day of the season, coming from behind to win 2-1 win away at Gorleston with Wayne Goddard scoring the winner in the 76th minute. The victory meant that title rivals Wroxham, who still had a game in hand against Warboys Town, could not catch them. Histon's victory gained them promotion to the Southern Football League and also saved Felixstowe Port & Town from relegation as, had Wroxham won, they would not have been promoted.[2]
| Competition: | Eastern Counties Football League Division One |
| Season: | 1999–2000 |
| Winners: | Tiptree United |
| Promoted: | Ely City Tiptree United |
| Matches: | 306 |
| Total Goals: | 1003 |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
Division One featured 16 clubs which competed in the division last season, along with two new clubs: