Last year's finalists Rudar and Mogren received a bye to the Second Round. The remaining 14 matches were played on 24 August 2011, with the exception of the Blue Star vs Čelik match, which was played the next day.
The 14 winners from the First Round and last year's cup finalists, Rudar and Mogren, compete in this round. Starting with this round, all rounds of the competition will be two-legged except for the final. The first legs were held on 14 September 2011, while the second legs were held on 28 September 2011.