The 2003 CAF Cup was the 12th and final edition of the African continental club competition for runners up of the respective domestic leagues.

It was won by Moroccan team Raja Casablanca who beat Cotonsport Garoua from Cameroon over two legs in the final.

In following seasons, the CAF Cup was merged with the African Cup Winners' Cup to form the CAF Confederation Cup.

1LISCR withdrew before the first leg and were subsequently banned for 3 years by CAF.

Saint Michel United win 1-0 on aggregate Green Buffaloes win 3-2 on aggregate 1-1 on aggregate, Black Rhinos win on away goals Kiyovu Sport win 3-1 on aggregate Al-Nasr win 1-0 on aggregate 0-0 on aggregate, SONACOS win 5-4 on penalties Raja Casablanca win 7-2 on aggregate FC 105 Libreville win 4-3 on aggregate Club Africain win 2-1 on aggregate Jeunesse Club d'Abidjan win 2-1 on aggregate 0-0 on aggregate, Cotonsport Garoua win 4-2 on penalties 2-2 on aggregate, Mamelodi Sundowns win 9-8 on penalties DC Motema Pembe win 7-1 on aggregate Green Buffaloes win 7-1 on aggregate Black Rhinos win 2-1 on aggregate 1-1 on aggregate, JS Kabylie win on away goals Al-Ahly win 4-1 on aggregate Raja Casablanca win 7-3 on aggregate Club Africain win 6-2 on aggregate Cotonsport Garoua win 2-1 on aggregate Enugu Rangers win 1-0 on aggregate Raja Casablanca win 2-0 on aggregate