The youngster had a breakout campaign last year scoring 10 league goals but has struggled for game time this season.
He made only four substitute appearances for the Reds this year and his ongoing groin injury was a major problem.
The Gunners expect their academy player to return to full fitness as early as December given the number of games Arsenal will face after the World Cup.
He is a crucial member of Arteta’s XI and the manager will only have a few options to replace him.
Arsenal faces Tottenham Hotspur at the Emirates on Saturday afternoon.
“Following a significant setback at our Premier League match against Manchester United … and after further specialist consultations and discussions with our medical team, Emile underwent surgery to repair a damaged tendon in his groin,” Arsenal said in a statement.
“This successful surgery took place in London in the past few days and Emile’s rehabilitation programme is already underway. We are hopeful that Emile will return to full training in December.”
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