Alashkert from the First Division played in the first round against Banants from the Premier League. The rest of the teams received a bye to the quarter finals. The first leg was played on 14 November, with the second leg took place on 28 November 2012.
The remaining seven Premier League clubs entered the competition in this round, together with the winner from the first round. The first legs were played on 1 March 2013, while the second legs were played on 12 March 2013.