The 1998–99 Spartan South Midlands Football League season was the 2nd in the history of Spartan South Midlands Football League.
| Competition: | Spartan South Midlands Football League Premier Division |
| Season: | 1998–99 |
| Winners: | Barkingside |
| Relegated: | Brimsdown Rovers |
| Matches: | 506 |
| Total Goals: | 1632 |
| Prevseason: | 1997–98 North 1997–98 South |
| Nextseason: | 1999–2000 |
At the end of the previous season regional Premier Division North and Premier Division South merged with the first ten clubs from both divisions to form new Premier Division. The Premier Division featured 23 clubs.
| Competition: | Spartan South Midlands Football League Senior Division |
| Season: | 1998–99 |
| Winners: | Holmer Green |
| Promoted: | Holmer Green Hanwell Town Biggleswade Town |
| Relegated: | Winslow United |
| Matches: | 462 |
| Total Goals: | 1608 |
| Prevseason: | 1997–98 |
| Nextseason: | 1999–2000 |
At the end of the previous season regional Premier Division North and Premier Division South merged with the first ten clubs from both divisions to form new Premier Division, while all other Premier divisions clubs relegated to the Senior Division. The Senior Division featured eleven clubs which competed in the division last season, along with eleven new clubs.
At the end of the season Milton Keynes were renamed Bletchley Town.
| Competition: | Spartan South Midlands Football League Division One |
| Season: | 1998–99 |
| Winners: | Bridger Packaging |
| Promoted: | Bridger Packaging Ampthill Town |
| Matches: | 272 |
| Total Goals: | 1079 |
| Prevseason: | 1997–98 North |
| Nextseason: | 1999–2000 |
Division One featured eleven clubs which competed in previous season Division One North, along with six new clubs.