1. ^1 One hundred and sixteen of the one hundred and eighteen teams competing in the 2003–04 Terceira Divisão, played in this round. Benfica B were unable to compete in the domestic cup competition due to the possibility of encountering their senior side in the competition. Queluz also did not participate.
2. ^2 Fifty four of the fifty nine teams competing in the 2003–04 Segunda Divisão, played in this round. Académica de Coimbra B, Braga B, Marítimo B, Porto B and Sporting CP B were unable to compete in the domestic cup competition due to the possibility of encountering their senior side in the competition. Queluz also did not participate.
For the first round draw, teams were drawn against each other in accordance to their geographical location. The draw was split up into four sections: teams from the north, the center, the south and the Azores region.[6] All first round cup ties were played on the 7 September.[7][8] Due to the odd number of teams at this stage of the competition, Rabo de Peixe progressed to the next round due to having no opponent to face at this stage of the competition. The first round of the cup saw teams from the Terceira Divisão (IV) start the competition alongside some teams who registered to participate in the cup from the Portuguese District Leagues (V).
For the second round draw, teams were drawn against each other in accordance to their geographical location. The draw was split up into three sections: teams from the north, the center and the south. Ties were played on the 28 September.[9][10] The second round saw teams from the Portuguese Second Division (III) enter the competition.
The draw for the third round took place on the 2 October.[11] Ties were played on the 11–12 October.[12][13] The third round saw teams from the Liga de Honra (II) enter the competition.
Ties were played on the 17 December.[16][17]Felgueiras won their fifth round cup tie against Vilafranquense,[18] but their win was overturned and Vilafranquense progressed to the next round due to Felgueiras' coach appearing at the tie to manage his side when he was supposed to be suspended.[19] Due to the odd number of teams involved at this stage of the competition, Braga qualified for the quarter-finals due to having no opponent to face at this stage of the competition.
Ties were played on the 14–21 January.[20][21] Due to the odd number of teams involved at this stage of the competition, Benfica qualified for the quarter-finals due to having no opponent to face at this stage of the competition.