Royals' keeper sustained serious damage to his shoulder when he collided with a goalpost during Reading's 1-1 draw at QPR on November 3.
Now, efforts to repair the damage appear to have failed, with the 22-year-old due to go under the knife early next week.
McCarthy tweeted this afternoon: "On route back home from London, was expecting the outcome with the specialist. Surgery on Monday. My season over! #Raging"
The news is a bitter blow for Reading having made McCarthy their first-choice keeper earlier this season.
Adam Federici will now continue between the sticks, with Stuart Taylor and Mikkel Anderson - recently back from a loan spell at Portsmouth - as back-up.
Federici will now keep his place in the starting line-up this Saturday when Reading host Manchester United at Madejski Stadium (5.30pm ko).