The 22-year-old, capped once by England in a friendly against Ecuador last summer, has been troubled by the problem for almost a year.
Flanagan missed all of Liverpool???s pre-season fixtures before the current campaign because of a build up of fluid on his knee.
He underwent surgery to rectify the problem last September, and finally returned to action in a friendly match in March.
But the Reds full-back has suffered a reaction and has undergone further surgery which will keep him on the sidelines until at least November.
Flanagan is out of contract at Anfield at the end of the season, but has been in talks over a new deal in recent months.