[3] The final arrangements of the zonal qualifiers were decided later due to the delays caused by the COVID-19 pandemic.

Tunisia hosted the 2020 UNAF U-20 Tournament, which also served as the qualifiers for the Africa U-20 Cup of Nations, between 15 and 27 December 2020.

[5] The five teams were placed in one group, with the winners and the runners-up qualifying for the final tournament.

The WAFU-UFOA Zone B qualifiers for the Africa U-20 Cup of Nations were initially planned to be hosted by Burkina Faso, but were later shifted to Togo due to the COVID-19 pandemic, with the matches scheduled to be played between 18 November–2 December.

On 7 November, Togo announced that they would not be able to host the tournament due to a resurgence of COVID-19 cases in the country, with the outbreak located in the Lomé area.

[13] On 17 November, it was announced that the regional qualifiers would now be played in Benin between 5 and 19 December.

The UNIFFAC qualifiers for the Africa U-20 Cup of Nations were held in Equatorial Guinea between 15 and 22 December 2020.

The CECAFA qualifiers for the Africa U-20 Cup of Nations were initially planned to be hosted by Sudan in October–November 2020 but were then later shifted and held in Tanzania between 22 November–2 December 2020.

[19] The matches were played at Karatu (Black Rhino Academy) and Arusha (Sheikh Amri Abeid Memorial Stadium).

The COSAFA qualifiers for the Africa U-20 Cup of Nations were initially planned to be hosted by Mauritius, but were later shifted to South Africa after Mauritius withdrew as hosts due to the COVID-19 regulations.