The 2023–24 CAF Confederation Cup knockout stage started on 31 March with the quarter-finals and ended on 19 May 2024 with the second leg of the final to decide the champions of the 2023–24 CAF Confederation Cup.
The team that scored more goals on aggregate over the two legs advanced to the next round.
If away goals were also equal, then extra time was not played and the winners were decided by a penalty shoot-out (Regulations III.
The bracket of the knockout stage was determined as follows: The bracket was decided after the draw for the knockout stage, which was held on 12 March 2024, 14:00 CAT (UTC+2) at the CAF headquarters in Cairo, Egypt.
RS Berkane won on walkover after USM Alger withdrew.