The 2008–09 Northern Counties East Football League season was the 27th in the history of Northern Counties East Football League, a football competition in England.
| Competition: | Northern Counties East Football League Premier Division |
| Season: | 2008–09 |
| Winners: | Mickleover Sports |
| Promoted: | Mickleover Sports |
| Relegated: | Eccleshill United |
| Matches: | 380 |
| Total Goals: | 1364 |
| Prevseason: | 2007–08 |
| Nextseason: | 2009–10 |
The Premier Division featured 17 clubs which competed in the previous season, along with three new clubs.
| Competition: | Northern Counties East Football League Division One |
| Season: | 2008–09 |
| Winners: | Scarborough Athletic |
| Promoted: | Rainworth Miners Welfare Scarborough Athletic |
| Matches: | 342 |
| Total Goals: | 1203 |
| Prevseason: | 2007–08 |
| Nextseason: | 2009–10 |
Division One featured 13 clubs which competed in the previous season, along with six clubs:
Also, Leeds Met Carnegie changed name to Leeds Carnegie.