The 1988–89 Northern Counties East Football League season was the 7th in the history of Northern Counties East Football League, a football competition in England.
| Competition: | Northern Counties East Football League Premier Division |
| Season: | 1988–89 |
| Winners: | Emley |
| Promoted: | Emley |
| Matches: | 272 |
| Total Goals: | 822 |
| Prevseason: | 1987–88 |
| Nextseason: | 1989–90 |
The Premier Division featured 17 clubs which competed in the previous season, no new clubs joined the division this season.
| Competition: | Northern Counties East Football League Division One |
| Season: | 1988–89 |
| Winners: | Sheffield |
| Promoted: | Sheffield |
| Relegated: | Bradley Rangers Pilkington Recreation |
| Matches: | 240 |
| Total Goals: | 682 |
| Prevseason: | 1987–88 |
| Nextseason: | 1989–90 |
Division One featured 14 clubs which competed in the previous season, along with two new clubs, promoted from Division Two:
| Competition: | Northern Counties East Football League Division Two |
| Season: | 1988–89 |
| Winners: | Ossett Town |
| Promoted: | Ossett Town Liversedge |
| Matches: | 182 |
| Total Goals: | 604 |
| Prevseason: | 1987–88 |
| Nextseason: | 1989–90 |
Division One featured 12 clubs which competed in the previous season, along with two new clubs: