The 1999 S.League was the fourth season of the S.League, the top professional football league in Singapore.

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.

As 1999 S.League champions, Home United qualified to compete in the 2000–01 Asian Club Championship.

The club reached the second round of the East Asian half of the competition, defeating Polícia de Segurança Pública of the Campeonato da 1ª Divisão do Futebol 11–0 on aggregate before being defeated 6–1 on aggregate in the second round by Shandong Luneng Taishan of the Chinese Jia-A League.