It began on 22 July 2012 with the preliminary round and ended with the final on 18 May 2013.

FK Baumit Jablonec prevailed at the 17 May 2013 Cup and qualified for the 2013–14 UEFA Europa League.

12 teams from the Czech First League enter at this stage.

The top four teams from last season's Czech First League enter at this stage.

The fourth round was scheduled to be played on 31 October and 28 November 2012.