Last year's Supercopa was marked by ill-feeling between the clubs highlighted when Mourinho poked new Barca boss Tito Vilanova, then an assistant to Pep Guardiola, in the eye during a pitchside scuffle.
That set the tone for a season of bad blood between Spain's most high-profile clubs, which ultimately ended with Madrid reclaiming the La Liga crown after four years.
Despite that Mourinho on Wednesday said the result over the two legs would have no bearing on the season - saying only that he would prefer to again lose the competition if it meant winning back-to-back league crowns.
"The Supercopa is a competition we want to win, but it will have no bearing on the development of the season," he told a press conference.
"If I had the choice I would choose to lose now and win La Liga as we did last year.
"It is the least important competition of the four that we play and in my opinion it has no consequence on the season.
"It is like a summer tournament played in Italy between rival teams but you do still always want to win - and our opponents too."
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Mourinho confirmed that he would be without Pepe after the Portugal defender was taken to hospital having suffered a head injury during the season-opening 1-1 draw against Valencia at the weekend.
Pepe collided heavily with goalkeeper Iker Casillas and, while he was released from hospital on Monday, will sit out Thursday's game with Raul Albiol coming in.
"Pepe will not play, it isn't humane to risk a player for a game of football, however important it may be," Mourinho said.
"He is recovering very well and we think he will be back again on Sunday without any type of risk. Albiol will play."
The match will be Vilanova's first major test since he took over as manager following Guardiola's decision to leave at the end of last season.
Vilanova kicked off his tenure with an impressive 5-1 win over Real Sociedad on Sunday and he could be further boosted on Thursday night with new signing Alex Song available following his move from Arsenal.
Mourinho is expecting a similar Barca team to the one Vilanova inherited, in what will be midfielder Cesc Fabregas' 50th for the Catalans.
"There may be a few new details but essentially nothing has changed," Mourinho said.
"It is the same Barca we know - a quality team with great players."