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1st S.League title
|Asian Club Championship||Home United|
|Goals scored||410 (3.11 per match)|
|Top goalscorer||Mirko Grabovac (23)|
|Biggest home win||Singapore Armed Forces 7-0 Woodlands Wellington
(17 April 1999)
|Biggest away win||Clementi Khalsa 0-6 Balestier Central
(19 May 1999)
|Highest scoring||Tampines Rovers 4-4 Gombak United
(24 September 1999)
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.
|Balestier Central||Toa Payoh Stadium||3,900||Toa Payoh|
|Geylang United||Bedok Stadium||3,900||Bedok|
|Gombak United||Bukit Gombak Stadium||3,000||Bukit Batok|
|Clementi Khalsa||Clementi Stadium||4,000||Clementi|
|Jurong||Jurong East Stadium||2,700||Jurong East|
|Home United||Bishan Stadium||4,000||Bishan|
|Marine Castle||Hougang Stadium||3,000||Hougang|
|Singapore Armed Forces||Jurong Stadium||6,000||Jurong|
|Sembawang Rangers||Yishun Stadium||3,400||Yishun|
|Tampines Rovers||Tampines Stadium||3,600||Tampines|
|Tanjong Pagar United||Queenstown Stadium||3,800||Queenstown|
|Woodlands Wellington||Woodlands Stadium||4,300||Woodlands|
Each club is allowed to have up to a maximum of 4 foreign players.
|1||Home United||22||15||6||1||42||16||+26||51||Qualification to 2000–01 Asian Club Championship first round|
|2||Singapore Armed Forces||22||14||7||1||63||24||+39||49|
|3||Tanjong Pagar United||22||11||8||3||40||25||+15||41|
|12||Marine Castle United||22||3||3||16||21||56||−35||12|
Rules for classification: 1) points; 2) goal difference; 3) number of goals scored
As 1999 S.League champions, Home United qualified to compete in the 2000–01 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 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.