The clubs played a double round-robin for a total of four games each.
Universidad de El Salvador were disqualified from this season's competition for failing to complete paperwork to be involved in any division, therefore making them ineligible.
The draw for the round 16 was set to occur on 3 April 2017, but was postponed.
[6] Following discussion instead having a round robin competition they decided to change it to a single round knockout quarter finals.
The round included three team from tercera division still in the competition, Juventud Cara Sucia, Sensuntepeque and CD Chaguite who were the lowest-ranked team in this round.