The 1998–99 Northern Counties East Football League season was the 17th in the history of Northern Counties East Football League, a football competition in England.
| Competition: | Northern Counties East Football League Premier Division |
| Season: | 1998–99 |
| Winners: | Ossett Albion |
| Promoted: | Ossett Town |
| Relegated: | Pickering Town Pontefract Collieries |
| Matches: | 380 |
| Total Goals: | 1287 |
| Prevseason: | 1997–98 |
| Nextseason: | 1999–2000 |
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: | 1998–99 |
| Winners: | Harrogate Railway Athletic |
| Promoted: | Brodsworth Miners Welfare Harrogate Railway Athletic |
| Matches: | 156 |
| Total Goals: | 556 |
| Prevseason: | 1997–98 |
| Nextseason: | 1999–2000 |
Division One featured 12 clubs which competed in the previous season, along with one new club:
For first division teams