The group stage of the 2013 AFC Cup was played from 26 February to 1 May 2013. A total of 32 teams competed in the group stage.
The draw for the group stage was held on 6 December 2012, 15:00 UTC+8, at the AFC House in Kuala Lumpur, Malaysia. The 32 teams were drawn into eight groups of four. Teams from the same association could not be drawn into the same group.
The following 32 teams (16 from West Asia Zone, 16 from East Asia Zone) were entered into the group stage draw, which included the 31 automatic qualifiers and the qualifying play-off winner, whose identity was not known at the time of the draw:
Al-Muharraq (Bahrain) withdrew after the draw was held. As a result, Regar-TadAZ (Tajikistan), which were initially to enter the qualifying play-off, instead directly entered the group stage, and only two teams participated in the qualifying play-off.
In the group stage, each group was played on a home-and-away round-robin basis. The winners and runners-up of each group advanced to the round of 16.
The teams are ranked according to points (3 points for a win, 1 point for a tie, 0 points for a loss). If tied on points, tiebreakers are applied in the following order:
The matchdays were 5–6 March, 12–13 March, 2–3 April, 9–10 April, 23–24 April, and 30 April–1 May 2013.