The group stage of the 2006 CAF Confederation Cup was played from 12 August to 28 October 2006. A total of eight teams competed in the group stage.[1]
In the group stage, each group was played on a home-and-away round-robin basis. The winners of each group advanced directly to the final.
| Team | Pts | Pld | W | D | L | GF | GA | GD | |
|---|---|---|---|---|---|---|---|---|---|
 FAR Rabat | 13 | 6 | 4 | 1 | 1 | 9 | 5 | 4 | Final |
| Olympique Khouribga | 10 | 6 | 3 | 1 | 2 | 6 | 4 | 2 | |
 Petro Atlético | 8 | 6 | 2 | 2 | 2 | 10 | 7 | 3 | |
| GD Interclube | 3 | 6 | 1 | 0 | 5 | 3 | 12 | -9 |
| Home | Score | Away | |
|---|---|---|---|
| GD Interclube | 1 - 3 | Petro Atlético | |
| FAR Rabat | 3 - 1 | Olympique Khouribga | |
| Olympique Khouribga | 1 - 0 | GD Interclube | |
| Petro Atlético | 1 - 1 | FAR Rabat | |
| FAR Rabat | 2 - 0 | GD Interclube | |
| Olympique Khouribga | 1 - 0 | Petro Atlético | |
| GD Interclube | 0 - 2 | FAR Rabat | |
| Petro Atlético | 1 - 1 | Olympique Khouribga | |
| Olympique Khouribga | 2 - 0 | FAR Rabat | |
| Petro Atlético | 4 - 1 | GD Interclube | |
| GD Interclube | 1 - 0 | Olympique Khouribga | |
| FAR Rabat | 2 - 1 | Petro Atlético |
| Team | Pts | Pld | W | D | L | GF | GA | GD | |
|---|---|---|---|---|---|---|---|---|---|
 Étoile Sahel | 18 | 6 | 6 | 0 | 0 | 15 | 3 | 12 | Final |
| Espérance | 8 | 6 | 2 | 2 | 2 | 10 | 7 | 3 | |
| FC Saint Eloi Lupopo | 4 | 6 | 1 | 1 | 4 | 8 | 12 | -4 | |
 Renacimiento FC | 4 | 6 | 1 | 1 | 4 | 6 | 17 | -11 |
| Home | Score | Away | |
|---|---|---|---|
| Étoile Sahel | 1 - 0 | Espérance | |
| FC Saint Eloi Lupopo | 5 - 1 | Renacimiento FC | |
| Espérance | 1 - 0 | FC Saint Eloi Lupopo | |
| Renacimiento FC | 0 - 2 | Étoile Sahel | |
| Étoile Sahel | 4 - 1 | FC Saint Eloi Lupopo | |
| Espérance | 5 - 0 | Renacimiento FC | |
| 0 - 1 | Étoile Sahel | ||
| Renacimiento FC | 1 - 1 | Espérance | |
| Espérance | 1 - 3 | Étoile Sahel | |
| Renacimiento FC | 3 - 0 | FC Saint Eloi Lupopo | |
| 2 - 2 | Espérance | ||
| Étoile Sahel | 4 - 1 | Renacimiento FC |