| Tournament details | |
|---|---|
| Host country | Rwanda |
| Dates | July 24 – August 7 |
| Teams | 12 (from CECAFA confederations) |
| Final positions | |
| Champions |  Rwanda B (1st title) |
| Runners-up |  Kenya |
| Tournament statistics | |
| Matches played | 20 |
| Goals scored | 34 (1.7 per match) |
The 1999 CECAFA Cup was the 23rd edition of the tournament. It was held in Rwanda, and was won by Rwanda B team. The matches were played between July 24–August 7.
Rwanda sent two teams: Rwanda A and Rwanda B.