The 21-year-old Brazilian defied Mourinho’s express advice when he sought, and accepted, a temporary move to the La Liga side, having spent all of last season on loan at Granada.
Pereira, signed as a youth player from PSV Eindhoven five years ago, has yet to start a league game for United but is so highly regarded that he was handed a new, long-term deal by Mourinho this summer, just as he decided to move elsewhere.
“His was a personal decision that I don’t agree with, a decision I don’t think honestly is the best decision for him, a decision that disappoints me,” Mourinho said at the team’s Carrington training base on Friday.
“He has the potential to be fighting for a position, fighting for opportunities and fighting to be a Manchester United player.”
Given the depth of the squad Mourinho has at his disposal this season, it is not hard to understand why Pereira might have thought he would be better served by moving elsewhere to gain more experience.
But Mourinho, who takes his table-topping side to Stoke on Saturday, added: “His decision can be considered a young player who wants to play every weekend but also a young player that is not ready to fight for something difficult.”
Mourinho also welcomed the decision made by Premier League clubs to bring forward the summer transfer window in 2018 to the Thursday before the new campaign kicks off.
But he is wary of the danger that some English clubs may lose players to foreign teams who can still sign stars until the end of August.
He said: “As the head coach of Manchester United, obviously I am in favour of that because if I focus just on the training process of course.
“I want to arrive, day one, I want to have my squad, my players, I want to work and travel with them in pre-season, I don’t want to be waiting for late decisions.
“But there is another perspective and I have to share the problems the board has and that is that obviously when the decision is not uniform around Europe and all the championships then we are opening a disadvantage for the English clubs.
“That was the reason why Manchester United voted against because there is another element – the market will be closed for us and is open for others and they can come to the English clubs.”
The Manchester United boss said he wanted a broader solution, adding: “I hope it goes to the perfect situation, which is to close for every championship and not just the Premier League.”