18 clubs that qualified through MNZ Regional Cups + 6 clubs from 2015–16 PrvaLiga that didn't qualify for European competitions will enter at this stage and will be drawn into 12 pairs.
Teams, qualified from the same regional cup cannot be drawn against each other.
Winners will be decided over one leg, with extra time and penalties if scores are level. Lower level teams are the hosts. If both teams from a pair are from the same level, hosting will be determined by the draw.
Round of 16
TBD
7 / 14 September 2016
8
12+4 → 8
12 first round winners will be joined by four 2015–16 PrvaLiga teams that qualified for European competitions, and will be drawn into 8 pairs.
Teams, qualified from the same regional cup cannot be drawn against each other.
Winners will be decided over one leg, with extra time and penalties if scores are level. Lower level teams are hosts. If both teams from a pair are from the same level, hosting will be determined by the draw.
Quarter-finals
TBD
19 & 26 October 2016
4
8 → 4
8 teams will be drawn into 4 pairs.
Winners will be decided over two legs on home and away basis with away goals rule being used. In case of a tie extra time and penalties will be used.
Semi-finals
TBD
5 & 12 April 2017
2
4 → 2
4 teams will be drawn into 2 pairs.
Winners will be decided over two legs on home and away basis with away goals rule being used. In case of a tie extra time and penalties will be used.
Final
N/A
30 May 2017
1
2 → 1
Winner will be decided in a single game at a venue that will be announced by NZS. Extra time and penalties will be used if the scores are level.