| 1. Hailu Mekonen | ETH | 3:39.73 | | 2. David Lelei | KEN | 3:40.46 | | 3. Fredrick Cheruiyot | KEN | 3:41.21 | | 4. Daniel Zegeye | ETH | 3:41.97 | | 5. Ali Hakimi | TUN | 3:43.04 | | 6. Julius Ogwang | UGA | 3:43.57 | | 7. Julius Achon | UGA | 3:45.40 | | 8. Bonaventure Niyonizigiye | BUR | 3:45.73 | | 9. Mahmu Aden Ibrahim | SOM | 3:46.67 | | 10.Lambert Ndayikeza | BUR | 3:47.53 | | 11.Paskar Owor | UGA | 3:53.33 | | -. Sammy Mutai | KEN | DNF |
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| Heats - First 4 and Best 4 progress. |
| Heat 1 | Team | time | | 1. Daniel Zegeye | ETH | 3:42.23 | | 2. Fredrick Cheruiyot | KEN | 3:42.29 | | 3. Julius Achon | UGA | 3:42.97 | | 4. Ali Hakimi | TUN | 3:43.11 | | 5. Julius Ogwang | UGA | 3:43.36 | | 6. Bonaventure Niyonizigiye | BUR | 3:43.84 | | 7. Lambert Ndayikeza | BUR | 3:47.68 | | 8. Yaccob Furtenato | ERI | 3:58.15 | | 9. Kelebone Makoetlane | LES | 4:06.87 | | -. Alexis Sharamgabo | RWA | DNF | | -. Chipako Chungu | ZAM | DNS | | -. Kondeabalo Pakpessan | TOG | DNS | | -. Moses Mumba | ZAM | DNS |
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| Heat 2 | Team | time | | 1. David Lelei | KEN | 3:48.89 | | 2. Sammy Mutai | KEN | 3:48.93 | | 3. Hailu Mekonen | ETH | 3:49.12 | | 4. Mahmu Aden Ibrahim | SOM | 3:49.58 | | 5. Paskar Owor | UGA | 3:49.84 | | 6. Faro Esau | RSA | 3:50.71 | | 7. Ali Elzaidi | LBA | 3:53.60 | | 8. Francis Munthali | MAW | 3:53.87 | | 9. Amanuel Woldeselassie | ERI | 3:58.69 | | 10.Mohau Lethoasa | LES | 3:59.90 | | -. Marc Leandro Jean | GAB | DNF | | -. Ruben Silwimba | ZAM | DNS | | -. Morko Hhawu | TAN | DNS | | -. Jose Lourenco | ANG | DNS |
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