The CAF Champions League 2006 started on 17 February 2006 with a preliminary round. The second leg of the final was played in Tunisia on 11 November. Al-Ahly won the tournament for the second time in a row with a late winner by Mohamed Aboutreika.
1 The tie between AS Port-Louis 2000 and Coin Nord was played over one leg only by mutual consent.
2Wallidan FC withdrew.
3CIVO United withdrew.
4CAPS United were later ejected from the competition.
5El Ahmedi withdrew.
1 The match was abandoned in the 9th minute of injury time in the first half with Hearts of Oak leading 2–0 after Saint-George SA walked off protesting the quality of the officiating. The tie was awarded to Hearts of Oak.
2CAPS United were ejected from the competition after the 1st leg when it was discovered that false information had been submitted for two Malawian players in their first round match against AS Inter Star; AS Inter Star were also re-instated.
The first legs were played on 29 September–1 October and the second legs on 14–15 October.
The final 2 legs were played on 29 October and 11 November.