The defender dislocated his shoulder when training at the Belviour Drive training ground ahead of the game against Luton Town a fortnight ago.
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McCarthy had surgery on the shoulder on Wednesday, and City manager Rob Kelly confirmed he would be without his captain for the rest of the season.
He said: "The operation went very well, but he won't play again this season. That's disappointing because he is a player for us who is a leader both on and off the pitch".
"But the most important thing is that he now gets himself right and he will be ready for the start of next season".
Even though City loose their captain, there is still good cover at the back. Patrick Kisnorbo and Gareth McAuley have been playing well together at the centre of the defence recently and there are players that Kelly can bring in, the likes of Richard Stearmen and Darren Kenton.
Kelly also confirmed that Stephen Hughes, Gareth McAuley and Matty Fryatt were back in training after injuries, and could be selected for Saturdays game with Coventry City, if there are no further reactions to their injuries.