The 1998–99 season was the 97th in the history of the Western Football League.
The league champions for the fourth time in their history were Taunton Town, but runners-up Tiverton Town took promotion to the Southern League.
The champions of Division One were Minehead Town.
[1] The Premier Division remained at 20 clubs after Chard Town and Torrington were relegated to the First Division.
Two clubs joined: The First Division remained at 19 clubs after Bishop Sutton and Yeovil Town Reserves were promoted to the Premier Division, and Crediton United left the league.