The defending champions were Dinamo Zagreb, having won their 12th title the previous year by defeating Osijek in the final.
Most of the top flight clubs entered the competition in the following round, scheduled on 26 September 2012, with the exception of Lokomotiva, RNK Split and Zadar, as their cup coefficient (determined by their cup record over the last five seasons) was too low to skip the preliminary round.
A total of 32 clubs entered the preliminary round: 21 regional cup winners organized at the county level and 11 regional cup finalists (from the top 11 counties with the greatest number of registered football clubs).
The draw for the first round was held on 30 August, where the club with the lowest cup coefficient hosts the one with the highest and so on.
It was the last stage of the competition employing the single-leg format, as from the quarter-finals onward all fixtures were double-legged events.