1999–2000 Copa Presidente

The Copa Presidente 1999–2000 is the first staging of the Copa El Salvador football tournament.

Qualified teams
The nine group winners and the three best runners-up from the group stage qualify for the final stage.

Semi-final teams
The three group winners and the best runners-up from the quarterfinals group stage qualify for the semi-final.

Final
 Aguila {{center|3-2|Firpo