The 1998–99 Spartan South Midlands Football League season was the 2nd in the history of Spartan South Midlands Football League.
The Premier Division featured 23 clubs.
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.
Division One featured eleven clubs which competed in previous season Division One North, along with six new clubs.