The Wales international will go under the knife on Thursday to repair a problem he sustained at Burnley on New Year's Day.
Lynch recently returned and played in three games before suffering a recurrence which forced him to miss last weekend's Yorkshire derby against Sheffield Wednesday.
"Losing Joel is a blow because he's been an integral part of the team this season and has performed very well," Town manager Mark Robins told the club's official website.
"The medical staff and Joel have been working hard to manage this issue together until the end of the season, but we've reached the point where it needs to get resolved.
"I know Joel will work hard on his rehabilitation and we're already looking forward to welcoming him back in a month's time."