Maribor were the defending champions, having won their ninth cup title in the 2015–16 edition.
The twelve winners were decided over one leg, with extra time and penalties if scores were level.
The eight winners were decided over one leg, with extra time and penalties if scores were level.
The draw for the round of 16 was held on 19 August 2016 at the Football Association of Slovenia headquarters in Kranj.
[3] In this phase of the competition the 12 clubs who advanced from the first round were joined by Domžale, Gorica, Maribor and Olimpija.