The 22-year-old appeared to be close to a permanent switch to Valencia this summer after impressing on loan during the 2017-18 campaign.
Pereira has been restricted to just five Premier League appearances for United since emerging from the academy four years ago, having also spent the 2016-17 season on loan with Granada.
"It was a very important year for me at Valencia and I learned a lot," Pereira told the official Red Devils website. "I had a lot of experiences out there and I am very happy to be back. I am ready to play.
"This pre-season is very important for the team. We have to prepare very well for what is coming up next and I am doing my best to get minutes, and to show that I am ready."
Pereira is under contract at Old Trafford until 2019.