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.
| 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) |
Rwanda sent two teams: Rwanda A and Rwanda B.
Group stage edit
Group A edit
| Team | Pts | Pld | W | D | L | GF | GA | GD |
|---|---|---|---|---|---|---|---|---|
| Rwanda (A)
|
4 | 2 | 1 | 1 | 0 | 4 | 1 | +3 |
 Tanzania
|
4 | 2 | 1 | 1 | 0 | 2 | 1 | +1 |
 Djibouti
|
0 | 2 | 0 | 0 | 2 | 2 | 6 | –4 |
Group B edit
| Team | Pts | Pld | W | D | L | GF | GA | GD |
|---|---|---|---|---|---|---|---|---|
 Burundi
|
4 | 2 | 1 | 1 | 0 | 3 | 0 | +3 |
 Uganda
|
4 | 2 | 1 | 1 | 0 | 2 | 0 | +2 |
 Somalia
|
0 | 2 | 0 | 0 | 2 | 0 | 5 | –5 |
Group C edit
| Team | Pts | Pld | W | D | L | GF | GA | GD |
|---|---|---|---|---|---|---|---|---|
 Ethiopia
|
4 | 2 | 1 | 1 | 0 | 2 | 0 | +2 |
 Sudan
|
2 | 2 | 0 | 2 | 0 | 1 | 1 | 0 |
 Zanzibar
|
1 | 2 | 0 | 1 | 1 | 1 | 3 | –2 |
Group D edit
| Team | Pts | Pld | W | D | L | GF | GA | GD |
|---|---|---|---|---|---|---|---|---|
| Kenya
|
6 | 2 | 2 | 0 | 0 | 2 | 0 | +2 |
| Rwanda B
|
1 | 2 | 0 | 1 | 1 | 1 | 2 | –1 |
 Eritrea
|
1 | 2 | 0 | 1 | 1 | 1 | 2 | –1 |
Rwanda B finished second on coin toss.