[1] PSCS Cilacap became champion after beating PSS Sleman 4-3 after extra time in the final.
[3] But later on, PS Badung Bali and Persires Rengat withdrew from the tournament.
All groups will play home and away round-robin tournament.
[7] ^1 Perssu Super Madura awarded 3-0 win over PSIM Yogyakarta that failed to host the match due to not get permission from the police[8] The knockout stage will be held on 9–22 December 2016.
All matches will be held in Gelora Bumi Kartini, Jepara Matches for Third Place Play-off will be played at 17 December 2016 and will be held in Manahan, Surakarta Matches for Final will be played at 22 December 2016 and will be held in Gelora Bumi Kartini, Jepara