The men's 5000 metres event at the 2006 African Championships in Athletics was held at the Stade Germain Comarmond on August 9.
| Rank | Name | Nationality | Time | Notes | |
|---|---|---|---|---|---|
| 14:03.41 | |||||
| 14:05.12 | |||||
| 14:05.20 | |||||
| 14:06.21 | |||||
| 14:07.39 | |||||
| 14:07.40 | |||||
| 14:09.60 | |||||
| 14:10.06 | |||||
| 14:11.27 | |||||
| 10 | 14:11.81 | ||||
| 11 | 14:13.98 | ||||
| 12 | 15:22.76 |