United's 2-0 win at Burnley in the Premier League on Sunday brings them within a point of fourth-placed City ahead of the derby clash at the Etihad Stadium.
But with the games coming thick and fast and injuries taking a toll on his team, Mourinho said he would rotate his squad again with an eye on the May 4 Europa League, semi-final, first-leg at Spanish club Celta Vigo.
Asked about the chance to overtake City with a win in the derby, the Portuguese said: "But if we beat Celta we go to the final.
"Yes it is important for us to play in the Champions League but this club wants trophies. We cannot give the club the Premier League. We have a 25 percent chance to win the Europa League and we have to put everything on it.
"I will rotate the players again, I will rest some players again
"At least in terms of expectation for the game, the emotions, it is better a derby with one point difference than with four," he said.
One player who could be missing on Thursday is French midfielder Paul Pogba who was replaced at the end of Sunday's game.
Read the full article on eurosport.co.uk: Mourinho focused more on Europa League than City derby