| Rank | Heat | Nation | Athletes | Time | Notes |
| 1 | 1 |  Ivory Coast | Gnamien Nehemie N'Goran, Ismael Koné, Jacky Yapo Uleich Adzeu, Kouadio Éric Kouame | 39.53 | Q |
| 2 | 1 |  Senegal | Boubacar Drame, Mamadou Fall Sarr, Omar Ndoye, Moulaye Sonko | 39.61 | Q |
| 3 | 1 |  Liberia | Akeem Sirleaf, Emmanuel Matadi, Jabez Reeves, John Sherman | 40.00 | |
| 1 | 2 |  Botswana | Thapelo Monaiwa, Mothusi Boitshwarelo, Tumo Stagato van Wyk, Letsile Tebogo | 38.7 | Q |
| 2 | 2 |  South Africa | Bayanda Walaza, Sinesipho Dambile, Bradley Nkoana, Benjamin Richardson | 39.0 | Q |
| 3 | 2 |  Kenya | Meshack Babu, Mike Nyang'au, Mark Odhiambo, Samuel Waweru | 39.4 | q |
| 4 | 2 |  Namibia | Hatago Murere, Elvis Gaseb, Onesmus Nekundi, Gilbert Hainuca | 39.7 | q |
| 5 | 2 |  Cameroon | Ibrahima Hamayadji, Raphael Ngaguele Mberlina, Emmanuel Eseme, Appolinaire Yimra | 40.4 | |
| 1 | 3 |  Ghana | Fuseini Ibrahim, Isaac Botsio, Edwin Gadayi, Abdul-Rasheed Saminu | 39.15 | Q |
| 2 | 3 |  Nigeria | Alexander Chukwukelu, Emmanuel Ifeanyi Ojeli, Alaba Akintola, Usheoritse Itsekiri | 39.52 | Q |
| 3 | 3 |  Gambia | Sengan Jobe, Alieu Joof, Ebrahima Camara, Adama Jammeh | 39.79 | |
| 4 | 3 |  Eswatini | Mcebo Mkhaliphi, Mlandvo Maziya, Sibusiso Matsenjwa, Thandaza Zwane | 39.82 | |
| 5 | 3 |  Benin | Rémi Adandjo, Jerome Kounou, Jules Waiga, Didier Kiki | 42.41 | |
| 3 |  Zimbabwe | Dickson Kamungeremu, Gerren Muwishi, Tapiwa Makarawu, Ngoni Makusha | DNF | |
