Walker, who has played 14 games this year, will undergo an arthroscope on the lingering injury which he has managed for much of the season.
The 28-year-old will have surgery now, rather than at the end of the year, to ensure the problem does not cause further issues in the future.
Carlton football manager Andrew McKay said Walker had done well to contribute under duress through the year.
"Andrew's knee has been troubling him for a significant amount of the season, but to his credit he has managed to play through the pain and make a solid contribution for our team," McKay said on Carlton's website.
"While we have reduced Andrew’s training load and managed the injury as best we can, we believe it's his best interests to have an arthroscope now to ensure it doesn’t get any worse."
The Blues haven't seen the best of Walker in their difficult 2014 campaign, after he was moved to defence last year and enjoyed his most productive season.
The rebounding and dynamic half-back finished runner-up in the club's best and fairest and was named in the club's leadership group.
