The association ranking based on the UEFA country coefficients is used to determine the number of participating teams for each association:[6] The winners of the 2011–12 UEFA Europa League are given an additional entry as title holders if they do not qualify for the 2012–13 UEFA Champions League or Europa League through their domestic performance.

However, this additional entry is not necessary for this season since the title holders qualified for European competitions through their domestic performance.

When a place is vacated, it is redistributed within the national association by the following rules:[6] The labels in the parentheses show how each team qualified for the place of its starting round:[13][14] All draws are held at UEFA headquarters in Nyon, Switzerland unless stated otherwise.

[26] Matches in the qualifying, play-off, and knockout rounds may also be played on Tuesdays or Wednesdays instead of the regular Thursdays due to scheduling conflicts.

In the qualifying rounds and the play-off round, teams were divided into seeded and unseeded teams based on their 2012 UEFA club coefficients,[27][28][29] and then drawn into two-legged home-and-away ties.

[36] This was the first time a team from Azerbaijan qualified for the group stage of a UEFA competition.

AEL, Anzhi, Kiryat Shmona, Levante, Marítimo, Neftçi and Videoton all appeared in the group stage of a UEFA competition for the first time.

In the knockout phase, teams played against each other over two legs on a home-and-away basis, except for the one-match final.