The 20-year-old made his first-team debut for the club against Wigan in the FA Cup on Sunday.
And he also played in a reserves match against Everton on Monday.
Man United stars bring out 4x4s to tackle farm track to and from training
Thu, February 2, 2017
Manchester United stars were forced to roll out their fleet of off-road vehicles as they made their way to and from training down a dirty farm track
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Manchester United stars are forced to take a farm track to and from training
But United have confirmed the Portuguese keeper will face a "period of absence" due to the injury.
The Manchester Evening News say Pereira has injured his knee and is likely to be out for months.
Joel Pereira comes on for his debut against Wigan
Dean Henderson has been recalled from his loan spell at Grimsby Town to be the third choice keeper behind David De Gea and Sergio Romero.
Last weekend, Pereira expressed his delight at making his debut.
“It was amazing,” he told MUTV.
Joel Pereira could be out for several months
“Me and my family are very happy.
“I would like to thank the manager for this.
“It’s not every player that gets the opportunity to come on at Old Trafford, so thanks to the manager. It was fantastic.”