The 2012 Indonesia Super League U-21 second stage is contested by a total of 10 teams.
The draw for the group stage was held at the PT.
In each group, teams play each other home-and-away in a round-robin format, but all the match was held at the same stadium with a home tournament.
The winners and runners-up of each group advance to the semifinal.
All matches were played in Surajaya Stadium, Lamongan.