Pereira impressed for the Red Devils on their pre-season tour of the United States, and it had been thought that the 21-year-old would battle for a spot in Mourinho's first XI this season.
The attacker was not involved in the opening three weeks of the 2017-18 Premier League campaign, however, and decided to leave Old Trafford to join Valencia on a season-long loan.
Mourinho has revealed that "it was a personal decision" for Pereira to seek an exit, and the Portuguese has refused to hide his 'disappointment' at the youngster's call.
"It 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 told reporters.
"He has the potential to be fighting for a position, opportunities and to be a Manchester United player. His decision can be considered as a young player who wants to play every weekend but also a young player that is not ready to fight for something different and it's different to play in Manchester United's midfield.
"You have to be ready to fight for the position and I am disappointed he left. But it was his decision. I open the door, he has a long-term contract. We have the option to bring him back on January 1, so is not a drama but it is a decision which disappoints me a little bit."
Pereira signed a new two-year contract with United earlier this month.