The defender has become a key member of the first-team squad this season and with just one year remaining on his current deal, Rodgers is keen to make sure Flanagan's future is sorted sooner rather than later.
"He will definitely be given a new deal in the summer, no question," the Liverpool manager told reporters.
"He's been a revelation, and particularly in the big games. You can see the confidence he has now. He has made himself an important member of the squad."
Flanagan made his debut in 2011 under Kenny Dalglish.