The Timberwolves say Flynn underwent successful surgery Tuesday in Colorado. The team says typical recovery time is three to four months.
Flynn first was injured in the second-to-last game of last season. He missed the final game of the season and aggravated the injury while working out with the team before summer league play.
The Timberwolves signed veteran Luke Ridnour last week to a four-year deal. They traded Flynn's backup, Ramon Sessions, to Cleveland on Monday along with Ryan Hollins for point guards Delonte West and Sebastian Telfair.
The team plans to waive West, but Telfair may have a spot for the immediate future while Flynn recovers.