The 1999 S.League was the fourth season of the S.League, the top professional football league in Singapore. Teams played each other once both home and away, in a 22-match season.
The 1999 S.League was won by Home United, their first S.League title.
The league expanded again to 12 teams with the addition of a newly formed team, Clementi Khalsa who were based in Clementi and played their home games at the Clementi Stadium. Clementi Khalsa were formed in order to give an S.League representation to the Singaporean Sikh community.
Each club is allowed to have up to a maximum of 4 foreign players.
<onlyinclude></onlyinclude> As 1999 S.League champions, Home United qualified to compete in the 2000âÂÂ01 Asian Club Championship. This was their first appearance in continental competition. The club reached the second round of the East Asian half of the competition, defeating PolÃÂcia de Segurança Pública of the Campeonato da 1ê Divisão do Futebol 11âÂÂ0 on aggregate before being defeated 6âÂÂ1 on aggregate in the second round by Shandong Luneng Taishan of the Chinese Jia-A League.