The 22-year-old has made seven appearances for the the Royals this season but does not look likely to add to that tally after being told he needs surgery on his shoulder
The incident happened when McCarthy collided with the goalpost in Reading's 1-1 draw at QPR.
Since then, efforts to try and solve the problem have not been a success, meaning an operation is the only option left for the former England Under-21 international.
McCarthy tweeted on Thursday afternoon: "On route back home from London, was expecting the outcome with the specialist. Surgery on Monday. My season over! #Raging"
Australian Adam Federici will continue to replace McCarthy for the rest of the season, with Stuart Taylor and Mikkel Anderson as back up options.
Federici's next test will come when Manchester United visit the Madejski on Saturday.