The 23-year-old - who is on loan at the Britannia Stadium from Chelsea - sustained the problem during Saturday's 2-1 home defeat to Burnley in the Premier League and is now likely to be sidelined until the new year.
"He has a significant thigh injury which is likely to keep him out for several weeks," said assistant manager Mark Bowen.
There is better news for Marc Wilson, meanwhile, who picked up a hamstring problem before the international break and missed the clash with Burnley.
"Marc trained on Tuesday, albeit lightly, but he trained and will have more intensive training later in the week and hopefully he'll be available at the weekend," added Bowen.
Stoke visit Liverpool in the Premier League on Saturday.
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