A preliminary round was held in order to reduce the number of teams competing in the next round to 32. It consisted of 7 single-legged ties, with penalty shoot-out as decider, if the score was tied after 90 minutes. Appearing in this round were bottom 9 teams from 2011–12 Serbian First League, as well as 5 regional cup winners. The draw contained seeded and unseeded teams. Bottom 9 teams from 2011–12 Serbian First League (RFK Novi Sad, OFK Mladenovac, Kolubara, Čukarički, Banat, Radnički Sombor, Mladi Radnik, Sinđelić Niš and Srem) were set as seeded teams, with 5 regional cup winners(Dunav, Kovačevac, Timok, Jedinstvo Putevi and Trepča (KM)) being set as unseeded teams. After drawing 5 seeded-unseeded match-ups, remaining 2 fixtures were determined by regular draw, without seeds. The matches were played on 5 and 12 September 2012.

In this round, seven winners from the previous round will be joined by all 16 teams from Serbian Superliga from 2011–12, as well as top 9 teams from Serbian First League from 2011–12. The draw contained seeded and unseeded teams. 16 teams from 2011–12 Serbian SuperLiga(Partizan, Red Star, Vojvodina, Jagodina, Sloboda Užice, Radnički 1923, Spartak Subotica, OFK Beograd, Javor, Rad, Hajduk Kula, BSK Borča, Smederevo, Novi Pazar, Borac Čačak (II) and Metalac (II)) were set as seeded teams. Draw was held on 13 September 2012. The matches were played on 26 September 2012. No extra time was played if the score was tied after regular 90 minutes, with games going straight into penalties.