The 2012–13 Estonian Cup was the 23rd season of the Estonia's most prestigious football knockout tournament. The winner of the Cup qualifies for the first qualifying round of the 2013–14 UEFA Europa League. Flora won the competition after they defeated Kalju 3–1 in the final. First round The draw was made by Estonian Football Association on 26 May 2012, before the 2011–12 final of the same competition. League level of the club in the brackets. FC Helios is the only team that takes part from Rahvaliiga (RL) — a league organized by Estonian Football Association, but not part of the main league system. |- !colspan="3" align="center"|5 June |- !colspan="3" align="center"|6 June |- !colspan="3" align="center"|10 June |- !colspan="3" align="center"|12 June |- !colspan="3" align="center"|19 June |- !colspan="3" align="center"|20 June |- !colspan="3" align="center"|21 June |- !colspan="3" align="center"|26 June |- !colspan="3" align="center"|1 July |- !colspan="3" align="center"|2 July |- !colspan="3" align="center"|4 July |- !colspan="3" align="center"|6 July |- !colspan="3" align="center"|11 July Notes Note 1: JK Leisi withdrew from the competition. Note 2: SK Tääksi withdrew from the competition. Note 3: Tartu JK Tammeka II withdrew from the competition. Note 4: Kohtla-Järve FC Lootus won the match 4–1, but used a suspended player. Therefore, the match was awarded -:1 to FC Puuma. Byes These teams were not drawn and secured a place in the second round without playing: Meistriliiga (Level 1): Narva JK Trans, JK Sillamäe Kalev, Paide Linnameeskond Esiliiga (2): Rakvere JK Tarvas II Liiga (3): Paide Kumake, Keila JK, FC Nõmme United III Liiga (4): Põlva FC Lootos, Koeru JK, Saaremaa JK, Valga FC Warrior, JK Welco Elekter IV Liiga (5): Viimsi MRJK, Taebla JK, FC Pubi Trehv, Tartu Quattromed II Second round The draw for the second round was made on 27 June. |- !colspan="3" align="center"|11 July |- !colspan="3" align="center"|13 July |- !colspan="3" align="center"|17 July |- !colspan="3" align="center"|18 July |- !colspan="3" align="center"|19 July |- !colspan="3" align="center"|22 July |- !colspan="3" align="center"|24 July |- !colspan="3" align="center"|25 July |- !colspan="3" align="center"|30 July |- !colspan="3" align="center"|31 July |- !colspan="3" align="center"|7 August |- !colspan="3" align="center"|8 August |- !colspan="3" align="center"|14 August |- !colspan="3" align="center"|15 August Third round The draw for the third round was made on 2 August. Provisional match dates are between 21 and 31 August. |- !colspan="3" align="center"|21 August |- !colspan="3" align="center"|22 August |- !colspan="3" align="center"|28 August |- !colspan="3" align="center"|4 September |- !colspan="3" align="center"|5 September |- !colspan="3" align="center"|9 September |- !colspan="3" align="center"|12 September Notes Note 5: Saaremaa JK