The 1999 Liga Perdana 2 season is the second season of Liga Perdana 2. A total of ten teams participated in the season.^[1]

Selangor and Perlis were relegated from Liga Perdana 1 while TMFC and Kelantan TNB were promoted from Malaysia FAM League to a now increased total number of teams competing in the league from eight to become ten teams.^[1]

The season kicked off on 19 March 1999.^[1] Johor won the title and was promoted to Liga Perdana 1 alongside Selangor.

Ten teams competing in the second season of Liga Perdana 2.^[1]

• Johor (1999 Liga Perdana 2 champions)
• Selangor
• Johor FC
• Perlis
• Kelantan
• Malacca
• ATM
• TMFC
• NS Chempaka
• Kelantan TNB

1.Johor - 38 PTS (1999 Liga Perdana 2 Champions)

2.Selangor - 37 PTS (Promoted to Liga Perdana 1)

3.Johor FC - 33 PTS

4.Perlis - 31 PTS (Promoted to Liga Perdana 1)

5.Kelantan - 29 PTS

6.Malacca - 26 PTS

7.ATM - 25 PTS

8.TMFC - 24 PTS

9.NS Chempaka - 14 PTS

10.Kelantan TNB - 13 PTS

1999 Liga Perdana 1 winner
Johor 1st title