The 23-year-old former England Under-21 international made seven top flight appearances this season before picking up an injury in Reading's 1-1 draw with QPR at Loftus Road at the beginning of November.
McCarthy has now undergone surgery in London to rectify the problem and Head of Sports Medicine Luke Anthony recalled how the procedure went, while trying not to put any sort of timescale on the player's return.
"We had an encouraging MRI scan on the Monday after the QPR game," he told the club's official website.
"Then we saw a shoulder specialist the following day and he was also positive that Alex should be able to recover with a conservative rehab programme.
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"The most important thing is for Alex to make a full recovery and return in optimal condition. If that allows him to return before the end of the season then that is something we will try for."
Reading currently sit in 19th place in the Premier League table with nine points from their opening 14 games, four points adrift of safety and take on fellow strugglers Southampton at St Mary's on Saturday.