The 23-year-old played 30 minutes against Fleetwood Town last week and followed that up with another appearance at the Kirkby academy.
Flanagan has undergone two knee operations, in September 2014 and in April 2015, since his last competitive appearance on the final day of the 2013/14 season.
After so long on the sidelines he is now being eased back into competitive action, playing at right-back in these two appearances so far for the under-21s.
With his contract expiring this summer, having been handed a new one-year deal last summer, Flanagan faces a race against time to get back to match fitness and earn a new extension.
Having Flanagan available for first-team action would be a welcome boost to Jurgen Klopp‘s depleted ranks, with the local lad able to provide much needed cover both current full-backs, Nathaniel Clyne and Alberto Moreno.
“It was great to give Flanno 45 minutes after his half an hour against Fleetwood,” said U21s coach Michael Beale.
“He did very well and is looking stronger and he will now look to push on in the next few weeks and get some more minutes.”
Great performance from the 21s today against Morcombe first team. 4-0 kev Stewart was excellent as a No. 6 Jon Flanagan looked fit?? #LFC
— Rob Jones (@RobjonesLFC2) January 5, 2016
Also in action for the under-21s today was Ryan McLaughlin, who returned from his loan spell at Aberdeen last month due to a lack of playing time.
The versatile Northern Irishman has had his share of injuries over the last two years too and operated from the right of the three behind the forward.
Having returned to Merseyside early, McLaughlin was not eligible to play in registered matches until January, when his loan officially expired. He could add depth in the full-back areas should Klopp like what he sees.
Meanwhile, Brazilian attacking midfielder Allan Rodrigues de Souza lined up in the No. 10 role. He has completed a loan at Finnish side SJK and will now head out on loan again this month in order to secure a work permit.
Midfielder Kevin Stewart, who suffered injury while on loan at Swindon Town also made an appearance in the game, playing in midfield. It was his first outing since September.
Jose Enrique played the full match at left-back.
LFC U21s: Fulton; Flanagan (Virtue), Brewitt (Whelan), Polgar (O’Hanlon), Enrique; Chirivella (Lennon), Stewart; Mclaughlin (Hart), Allan, Wilson (Philipps); Trickett-Smith.
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