A total of 38 teams from 38 CAF associations qualified for the tournament after winning their respective premier domestic cups. Of the 38 teams that qualified for the tournament 2 did not participate in it;
Ethiopian club Coffee FC, who were set to appear in the First Round, withdrew before their first leg tie with AS Inter Star.
Burundian club AS Inter Star, who had received a bye into the Second Round following the withdrawal of Coffee FC, would themselves withdraw before their first leg tie with Power Dynamos.
Format
The tournament consisted of five rounds preceding a two-legged final.
Preliminary round - The 12 lowest ranked teams - whose rankings were determined by their association's performances at previous CAF club tournaments - were drawn against each other in 6 matches consisting of two-legs each.
First round - The 6 winners from the preliminary round were then drawn against the remaining 26 clubs, resulting in 16 matches consisting of two-legs each.
Second round - The 16 winners from the first round were then drawn against each other, resulting in 8 matches consisting of two-legs each.
Quarter-finals - The 8 winners from the second round were then drawn against each other, resulting in 4 matches consisting of two-legs each.
Semi-finals - The 4 victorious quarter-finalists were then drawn against each other in 2 semi-finals consisting of two-legs each.
Final - The victorious semi-finalists contested a two-legged final to determine the champion.
The away goals rule was used to determine the victors in the event of a match being tied over the two-legs. If it was not possible to determine a winner using the away goals rule, the tie went to a penalty shootout to determine the winner.
Preliminary round
The first legs were played on 30 & 31 January, and the second legs were played on 14 February 1999.
Matches
First round
The first legs were played from 12–14 March, and the second legs were played from 26–28 March 1999.
Matches
Second round
The first legs were played between from 30 April-2 May, and the second legs were played from 14–16 May 1999.
Matches
Quarter-finals
The first legs were played on 4 & 5 September, and the second legs were played from 19–26 September 1999.
Matches
Semi-finals
The first legs were played on 10 October, and the second legs were played on 23 & 24 October 1999.
Matches
Final
First leg
Second leg
Africa Sports won the two-legged final 2-1 on aggregate.
