The men's 5000 metres event at the 1999 All-Africa Games was held at the Johannesburg Stadium.[1]
| Rank | Name | Nationality | Time | Notes | |
|---|---|---|---|---|---|
| 13:49.06 | |||||
| 13:49.79 | |||||
| 13:50.40 | |||||
| 13:51.22 | |||||
| 13:51.32 | |||||
| 13:53.03 | |||||
| 14:01.21 | |||||
| 14:04.65 | |||||
| 14:06.26 | |||||
| 10 | 14:13.08 | ||||
| 11 | 14:17.59 | ||||
| 12 | 14:20.93 | ||||
| 13 | 14:21.90 | ||||
| 14 | 14:23.03 | ||||
| 15 | 14:32.18 | ||||
| 16 | 14:32.24 | ||||
| 17 | 14:35.76 | ||||
| 18 | 14:37.83 | ||||
| 19 | 14:45.16 | ||||
| 20 | 14:49.18 | ||||
| 21 | 14:53.28 | ||||
| 22 | 15:02.79 | ||||
| 23 | 15:10.10 | ||||
| 24 | 15:10.89 | ||||
| 25 | 15:18.31 | ||||
| 26 | 16:18.00 | ||||
| 27 | 16:48.99 | ||||