The 22-year-old missed the entire 2014/15 season after undergoing surgery following a build-up of fluid in his knee.
Flanagan made a full recovery, but aggravated the same problem in April and once again went under the knife.
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The academy graduate has been working hard behind the scenes to get himself fit and win a place back in the Liverpool team.
And Flanagan is hoping to return to full training in December and admits he's had to be mentally strong during a difficult few months.
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"It's been going well. It's obviously been a frustrating time since last year when I got the injury," he said.
"I'm back running now and hopefully I can push on and get back in the team in a couple of months.
"I've just got to progress and get myself fit, building up my leg strength. [December] is the aim - if all goes well that's the plan.
Flanagan's spirit doesn't appear to have wavered despite the various setbacks that he's received over the past couple of years.
"I'm always there supporting the lads, you always want to be playing but you can't be and you've got to give the lads the support.
"You've got to stay positive. It's mentally tough, but I'm mentally strong."
Flanagan was a key part of Brendan Rodgers' side who went within a whisker of winning the Premier League title in 2014.
He was admired by supporters, who were impressed by his die-hard attitude and commitment.
A right-back by trade, Flanagan often slotted in on the left-hand side of defence under Rodgers and adapted to the role with minimal fuss.
Whilst sitting on the sidelines, Flanagan has witnessed a number of new faces arrive at Anfield who also play a similar role as him.
Nathaniel Clyne joined for £12 million from Southampton in the summer and has been Liverpool's regular right-back this term.
Alberto Moreno arrived last year from Seville and Joe Gomez also moved from Charlton earlier this year.
Gomez, however, tore his ACL in England Under 21's 2-0 win against Kazakhstan earlier this week and is expected to miss the rest of the season.
He's sidelined with an injury similar to Flanagan's, who has given his team-mate some valuable advice for a speedy recovery.
"I'm devastated for him, I know what it's like to be in his situation with a long-term injury," he added.
"I spoke to him yesterday and just told him to stay positive and if he ever needs any advice to come and see me, don't hesitate.
"I know it's going to be tough for him but he's got to stay positive."