The Barcelona trainer was hoping to avoid a potentially tricky tie in Andalucia against the Segunda Division side but insists the Catalans will be suitably motivated for the clash.
The Liga leader travels to Andalucia on Wednesday to take on the team that knocked out Real Sociedad in the previous round, and Vilanova is wary of the less illustrious opponent, though he believes his players will not struggle to get in the right frame of mind for the match.
"I would say that it is increasingly difficult and that it is a complicated tie. I would rather play against a top team," he told a press conference. "They are not just words, it is how I feel about the match, and I would have preferred to play a Primera Liga team. Cordoba eliminated Real Sociedad and played good football.
"I am fortunate that my players love to play football. I have asked them and they are all ready."
Vilanova has chosen to rest Andres Iniesta, Victor Valdes and Adriano for the cup tie but refused to admit that the match is less important than Sunday's game against second-placed Atletico Madrid in the league.
"I do not think this week is more crucial than others," he said. "There are two major matches, with Cordoba and Atletico. At this club every game is crucial."
The 44-year-old also commented on Lionel Messi's achievement after he ended Gerd Muller's record for number of goals in a calendar year on Sunday, and he said that the Argentina captain would be raring to add to his tally in midweek.
"The great thing about Messi is that he did in the youth team and he continues to do it in the first team, and that is the difficulty," he went on. "Messi always wants to play, against a second division team or the champions. He finds motivation in himself to excel and to be better every day."