The second stage of the 2013 Liga Indonesia Premier Division (LI) was played from 28 June to 27 August 2013. A total of twelve teams competed in the second stage.
The draw for the group stage was held in June 2013, at the Liga Indonesia House in Jakarta, Indonesia. The 12 teams were drawn into three groups of four.
In the group stage, each group was played on a home-and-away round-robin basis. The winners of each group and one best runners-up advanced to the semi-finals.
The teams are ranked according to points (3 points for a win, 1 point for a tie, 0 points for a loss). If tied on points, tiebreakers are applied in the following order:
The matchdays were 28 June, 2 July, 6 July, 19 August, 24/25 August, and 30 August 2013.