The qualifying rounds of the 2013 CAF Confederation Cup were played from 16 February to 2 June 2013, to decide the eight teams which advanced to the group stage.
[3] Rail Club du Kadiogo won 2–1 on aggregate and advanced to the first round.
Barrack Young Controllers II won 1–0 on aggregate and advanced to the first round.
Note: Al-Nasr played their home match in Tunisia due to security concerns in Libya.
Note: Second leg postponed after three players of DC Motema Pembe were killed in a car accident.
US Bitam advanced to the second round after Heartland arrived late for the second leg,[6] as per ruling made by the CAF.
Liga Muçulmana won on the away goals rule and advanced to the play-off round.
LLB Académic won the penalty shoot-out and advanced to the play-off round.
Étoile du Sahel won 7–2 on aggregate and advanced to the play-off round.
The draw for the play-off round was held on 7 May 2013, 12:00 UTC+2, at the CAF Headquarters in Cairo, Egypt.
Stade Malien won 6–0 on aggregate and advanced to the group stage.
CS Sfaxien advanced to the group stage after Enugu Rangers, which had originally won 1–0 on aggregate, was ruled by the CAF to have fielded an ineligible player in the second leg and thus disqualified.
ES Sétif won the penalty shoot-out and advanced to the group stage.
Étoile du Sahel won 4–3 on aggregate and advanced to the group stage.
Saint George won on the away goals rule and advanced to the group stage.