The 1999–2000 Northern Premier League season was the 32nd in the history of the Northern Premier League, a football competition in England. Teams were divided into two divisions; the Premier and the First.
| Competition: | Northern Premier League Premier Division |
| Season: | 1999–2000 |
| Winners: | Leigh RMI |
| Promoted: | Leigh RMI |
| Relegated: | Guiseley Winsford United |
| Matches: | 506 |
| Total Goals: | 1426 |
| Goals Per Game: | 2.82 |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
The Premier Division featured four new teams:
| Competition: | Northern Premier League Division One |
| Season: | 1999–2000 |
| Winners: | Accrington Stanley |
| Promoted: | Accrington Stanley Burscough |
| Relegated: | Flixton Whitley Bay |
| Matches: | 462 |
| Total Goals: | 1380 |
| Goals Per Game: | 2.99 |
| Prevseason: | 1998–99 |
| Nextseason: | 2000–01 |
Division One featured four new teams:
In the thirty-second season of the Northern Premier League Leigh RMI (as champions) were automatically promoted to the Football Conference. Guiseley and Winsford United were relegated to the First Division; these two clubs were replaced by relegated Conference side Altrincham, First Division winners Accrington Stanley and second placed Burscough. In the First Division Flixton and Whitley Bay left the League at the end of the season and were replaced by newly admitted North Ferriby United and Vauxhall Motors.
Challenge Cup
Teams from both leagues.
President's Cup
'Plate' competition for losing teams in the NPL Cup.
Chairman's Cup
'Plate' competition for losing teams in the NPL Cup.
Peter Swales Shield
Between Champions of NPL Premier Division and Winners of the NPL Cup.