The Liverpool defender has already missed the whole season so far with a knee injury picked up during pre-season and has now had to undergo another operation to help his recovery.
And that is expected to see the 22-year-old out of action until after the start of the 2015-16 campaign.
Previously capped by England at U19, U20 and Under-21 level, Flanagan’s form earned him a place on Roy Hodgson’s standby list for the World Cup in Brazil.
He was given a debut in the warm-up game with Ecuador in Miami and was also in contention for a place in Gareth Southgate’s U21s prior to his injury.
Flanagan, who is out of contract at Anfield this summer, is highly-rated by Reds boss Brendan Rodgers who has previously said the club will agree a new deal with him despite his problems this term.
"He is working his way back to fitness and when that happens I am sure the contract will get sorted out,” said Rodgers, prior to the full-back’s recent operation.
"He is a big part of the future here. He did remarkably well last year and showed he is player who can play for many years at this level."