All rounds were played on a home-and-away two-legged basis, with the higher-ranked team in the classification phase of each tie hosting the second leg.
The quarter-final pairings were pre-determined based on the teams' final position in the classification phase.
In the semi-finals the teams were re-seeded based also on their final position in the classification phase in order to determine the two pairings.
Comunicaciones were the defending champions, having won the Apertura 2023 tournament at the previous season.
The defending champions are Municipal, who had won the previous Clausura 2024 tournament.