The 1898–99 Northern Football League season was the tenth in the history of the Northern Football League, a football competition in Northern England.
| Competition: | Northern League |
| Season: | 1898–99 |
| Prevseason: | 1897–98 |
| Nextseason: | 1899–1900 |
| Competition: | Northern League Division One |
| Season: | 1898–99 |
| Winners: | Bishop Auckland |
| Matches: | 72 |
| Total Goals: | 246 |
The division featured 9 clubs which competed in the last season, no new clubs joined the league this season.
| Competition: | Northern League Division Two |
| Season: | 1898–99 |
| Winners: | Stockton St. John's |
| Matches: | 86 |
| Total Goals: | 291 |
The division featured 4 clubs which competed in the last season, along with six new clubs: