Intermediate teams from the Leinster Senior League, Munster Senior League and Ulster Senior League enter at this stage. In this round teams from the Leinster Senior League play each other, teams from the Munster Senior League play each other, and teams from the Ulster Senior League play each other. The draw was made on 4 September 2012 with ties to be played on the weekend of 30 September 2012. Extra-time and penalties will be played if necessary.
In this round teams from the winners of the first round from the Leinster Senior League play each other, Munster Senior League play each other, and teams from the Ulster Senior League play each other. The draw was made on 3 October 2012 with ties to be played on the weekend of 28 October 2012. Extra-time and penalties will be played if necessary.
Ulster
Munster
Leinster
* The match was abandoned when a Lucan United player was seriously injured. Greystones United were leading 2-1 at the time.
Third round
The draw for this round was made on 6 November 2012 by the FAI Domestic Committee. Ties are to be played on the weekend on 2 December. In this round teams from the Leinster Senior League, Munster Senior League, Ulster Senior League play each other. The 16 winners of the Third Round ties will progress to the Fourth Round and also qualify for the 2013 FAI Cup. If ties end in a draw after 90 minutes, a replay will be played in which the away side from the first match will have home advantage. In the replay if it remains a draw, extra-time will be played and if required, penalties.
Fourth round
The draw for this round was made on 4 December 2012 by the FAI Domestic Committee. The teams that have made it to the Fourth Round have qualified for the 2013 FAI Cup. If ties end in a draw after 90 minutes, a replay will be played in which the away side from the first match will have home advantage. In the replay if it remains a draw, extra-time will be played and if required, penalties. Parkvilla are the lowest ranked team remaining in the competition, playing in the 4th tier of the Leinster Senior League.
The draw for this round was made on 5 February 2013 by the FAI Domestic Committee. If ties end in a draw after 90 minutes, a replay will be played in which the away side from the first match will have home advantage. In the replay if it remains a draw after 90 minutes, extra-time will be played and if required, penalties. Parkvilla are the lowest ranked team remaining in the competition, playing in the 4th tier of the Leinster Senior League.
Semi Final
The draw for the semi finals were made on 5 March 2013 by the FAI Domestic Committee in the FAI Headquarters, Abbotstown. If ties end in a draw after 90 minutes, a replay will be played in which the away side from the first match will have home advantage. In the replay if it remains a draw after 90 minutes, extra-time will be played and if required, penalties.
