Athletics at the 1999 All-Africa Games Medal table Medal table

| Rank_ | Nation | Gold | Silver | Bronze | Total_ |
|---|---|---|---|---|---|
| 1 | Nigeria | 13 | 5 | 6 | 24 |
| 2 | South Africa | 11 | 11 | 8 | 30 |
| 3 | Ethiopia | 6 | 3 | 2 | 11 |
| 4 | Kenya | 5 | 4 | 8 | 17 |
| 5 | Tunisia | 2 | 2 | 1 | 5 |
| 6 | Senegal | 2 | 1 | 3 | 6 |
| 7 | Ghana | 2 | 0 | 4 | 6 |
| 8 | Cameroon | 1 | 4 | 1 | 6 |
| 9 | Egypt | 1 | 1 | 2 | 4 |
| 10 | Mauritius | 1 | 0 | 1 | 2 |
| 11 | Mozambique | 1 | 0 | 0 | 1 |
| 12 | Algeria | 0 | 8 | 1 | 9 |
| 13 | Madagascar | 0 | 2 | 1 | 3 |
| 14 | Zimbabwe | 0 | 1 | 1 | 2 |
| 15 | Tanzania | 0 | 1 | 0 | 1 |
| 15 | Togo | 0 | 1 | 0 | 1 |