[1] A total of 40 (out of 54) CAF member national teams entered qualification that was split into zones based on their regional affiliations and had its draw held on 9 October 2024 at CAF headquarters in Cairo, Egypt.
If the aggregate score is tied after the second leg, the away goals rule would be applied, and if still level, the penalty shoot-out would be used to determine the winner (no extra time would be played).
[3] On 22 November 2024, Libya withdrew from the tournament due to fixture congestion and concerns that the national team's participation would halt the league, hence the Libyan Football Federation prioritized the league schedule over the CHAN.
[4] On 28 November 2024, Tunisia also pulled out of the tournament following the clubs' rejection to the country's participation.
Because Congo did not present valid licenses for its players and fielded one who was not eligible,[6] Equatorial Guinea won 6–0 on aggregate.
Burundi won on walkover and advanced to the second round after Somalia withdrew prior to the first leg due to financial challenges.
[7] Ethiopia won on walkover and advanced to the second round after Eritrea withdrew prior to the first leg.
Zambia won on walkover and qualified to the final tournament after Mozambique withdrew prior to the first leg due to post-election violence.
[9] Following the withdrawals of Tunisia and Libya, it was decided to organise a second qualifier tournament between 7 'reengaged' teams: Algeria, Comoros, Egypt, Gabon, The Gambia, Malawi, South Africa to determine the final two slots.