1999 African Cup Winners' Cup

Association team allocation

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

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First round

The first legs were played from 12–14 March, and the second legs were played from 26–28 March 1999.

Matches

|} Notes: : Coffee FC withdrew before their first leg tie against AS Inter Star, handing AS Inter Star a walkover into the second round.

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

|} Notes: : AS Inter Star withdrew before their first leg tie against Power Dynamos, handing Power Dynamos a walkover into the second round.

Quarter-finals

The first legs were played on 4 & 5 September, and the second legs were played from 19–26 September 1999.

Matches

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Semi-finals

The first legs were played on 10 October, and the second legs were played on 23 & 24 October 1999.

Matches

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Final

Main article: 1999 African Cup Winners' Cup Final

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First leg

Second leg

Africa Sports won the two-legged final 2-1 on aggregate.