Barker has missed only one game this season, and that was due to suspension, but he has been unable to train during the week because of the problem and has only been playing in matches.
The 28-year-old will miss the remaining two games of the season against Bristol City and Reading.
"The operation went well, although a bit more damage was discovered than originally expected," manager Nigel Clough told the club`s official website.
"We are not putting a timeframe on when Shaun will be back but we look forward to seeing him in action next season..."
Source: PA
Source: PA