After playing a key role for Granada in La Liga last year, the 21-year-old attacking midfielder made the year-long switch to Valencia after renewing his contract at Old Trafford.
"Andreas Pereira was a personal decision that I don't agree with," Mourinho told reporters.
"A decision I don't think honestly is the best decision for him, a decision that disappoints me a little bit, because I think he has the potential to be here fighting for a position, for opportunities, and fighting to be a Manchester United player.
"I think his decision can be considered a decision of a young player who wants to play every weekend but can also be considered a decision by a young player that is not ready to fight for something difficult and it's difficult to play in the Manchester United midfield.
"You have to be ready to fight for a position and I am a bit disappointed that he left. But okay, it was his decision, I open the door for his decision, he has a long-term contract, we have the option to bring him back on January 1, so we have that situation under control.
"It is not a drama but is a decision that disappoints me a little bit."
Pereira joined United from PSV in 2011 and has since made 13 appearances for the first team in all competitions.