1999–2000 Copa Presidente
The Copa Presidente 1999–2000 is the first staging of the Copa El Salvador football tournament.
Participants
Group Stage
Three group were divided in 3 separate division. Each group was composed of four clubs.Knockout stage
Qualified teams
The nine group winners and the three best runners-up from the [|group stage] qualify for the final stage.| Team | Qualification | Divisional team | Zone |
| Atletico Balboa | Group Winner | Liga de Ascenso | Zona Oriental |
| Mar y Plata | Group Winner | Divisional team | Zona Oriental |
| Dragon | Group Winner | Divisional team | Zona Oriental |
| Aguila | Best second place team | Liga Mayor | Zona Oriental |
| LA Firpo | Group winner | Liga Mayor | Zona Central |
| San Luis | Group Winner | Divisional team | Zona Central |
| Atletico Marte | Group Winner | Divisional team | Zona Central |
| Chalatenango | Best second place team | Divisional team | Zona Central |
| ADET | Group winner | Divisional team | Zona Occidental |
| FAS | Group winner | Liga Mayor | Zona Occidental |
| Isidro Metapan | Group winner | Divisional team | Zona Occidental |
| Once Lobos | best second-place winner | Divisional team | Zona Occidental |
Second Leg
Aguila won on - aggregateLA Firpo won on - aggregate
Atletico Balboa won on - aggregate
ADET won on - aggregate
FAS won on - aggregate
''Atletico Marte won on 2-1 aggregate''
Semi-final teams
The three group winners and the best runners-up from the quarterfinals group stage qualify for the semi-final .| Team | Qualification | Divisional team | Zone |
| Atletico Balboa | Group Winner | Liga de Ascenso | Zona Oriental |
| Aguila | Best second place team | Liga Mayor | Zona Oriental |
| LA Firpo | Group winner | Liga Mayor | Zona Central |
| FAS | Group winner | Liga Mayor | Zona Occidental |