| Tourney Name: | CAF Champions League |
| Year: | 1999 |
| Size: | 200px |
| Dates: | 31 January – 12 December |
| Num Teams: | 41 |
| Associations: | 41 |
| Champion Other: |  Raja Casablanca |
| Count: | 3 |
| Second Other: |  ES Tunis |
| Matches: | 88 |
| Goals: | 233 |
| Prevseason: | 1998 |
| Nextseason: | 2000 |
The 1999 CAF Champions League was the 35th awarding of Africa's premier club football tournament prize organized by the Confederation of African Football (CAF), and the 3rd prize under the CAF Champions League format. Raja Casablanca of Morocco defeated ES Tunis of Tunisia on penalties in the final to win their third title.
See main article: 1999 CAF Champions League group stage.
See main article: 1999 CAF Champions League Final.
The top scorers from the 1999 CAF Champions League are as follows:
| Rank | Name | Team | Goals |
|---|---|---|---|
| 1 |  Hossam Hassan | Al Ahly | 6 |
| 2 |  Ishmael Addo | Hearts of Oak | 4 |
 Aruna Dindane | ASEC Mimosas | ||
| Venance Zézé | ASEC Mimosas | ||
| Mustapha Moustawdaa | Raja Casablanca | ||
| Walid Azaiez | ES Tunis | ||
| 7 | Mohamed Gouda | Al Ahly | 3 |
| Emmanuel Osei Kuffour | Hearts of Oak | ||
| Kingston Rinemhota | Dynamos Harare | ||
| Ronald Sibanda | Dynamos Harare |