The competing pairs were selected as a result of random drawing that took place on 2 September 2013.
* Note: Digenis Lakkoma even if have been defeated, qualified to the quarter-finals, as favored in the draw between the groups' finalists.
* Note: Kozani even if have been defeated, qualified to the quarter-finals, as favored in the draw between the groups' finalists.
In the Second Round of the competition (quarter-finals), the 6 group winners and two group finalists (selected randomly in a draw that took place on 19 December 2013) competed against each other in single knock-out matches at the home ground of the club favored by the draw.
In the Third Round of the competition (semi-finals), the four clubs advancing from the Quarter-finals competed in double knockout matches (away goals rule) and the two winners advanced to the final.