The defender, who has been out injured since March, went under the knife earlier this week to correct the problem.
"Rory McKeown had an operation yesterday (Wednesday). It seemed to be a success," said Kilmarnock boss Jimmy Nicholl. "It was just a wee clean-up, a tidy-up, but I think his season is over to be honest.
"The medical people might tell me something different but there are only four or five weeks left so I can't imagine Rory being involved."
Kilmarnock currently lie in seventh place in the Scottish Premier League.