The 1898–99 season was the seventh in the history of the Western Football League.
Swindon Town were the champions of Division One, and also competed in the Southern League during this season, along with Southampton and Bedminster.
Trowbridge Town and multiple champions Warmley also competed in both leagues, but both clubs disbanded during the season.
The Division Two champions for the first time were Staple Hill.
[1] Two new clubs joined Division One, which was reduced to seven clubs from eight after Bristol City, Reading and Eastleigh left.