The men's high jump event at the 2006 African Championships in Athletics was held at the Stade Germain Comarmond on August 13.
| Rank | Name | Nationality | Result | Notes | |
|---|---|---|---|---|---|
| 2.30 | PB | ||||
| 2.22 | |||||
| 2.22 | |||||
| 2.19 | |||||
| 2.15 | |||||
| 2.15 | |||||
| Serge Foungtcho | 2.10 | ||||
| Jude Sidonie | 2.05 | ||||
| 2.05 | |||||
| 10 | 2.05 | ||||
| 11 | Mathieu Gomis | 2.05 | |||
| 12 | Eugene Ernesta | 2.00 | |||
| 12 | Salomon Taure | 2.00 | |||
| Christopher Amankra | |||||
| Ahmed Farouk El-Zaher | |||||
| Mekombo Massanga |