He reached an agreement on a new contract with the Packers on Tuesday, a league source told ESPN NFL Insider Adam Schefter.
The deal came on the heels of a scheduled visit to the New York Giants, which was called off Tuesday.
Flynn, who began his career with Green Bay and served as Rodgers' backup from 2008 to 2011, returned to the team last season on Nov. 12 after backup quarterback Seneca Wallace sustained a groin injury the week after Rodgers went down.
Less than two weeks later, Flynn took over for Scott Tolzien and rallied the Packers from a 16-point deficit to tie the Minnesota Vikings on Nov. 24. He started the next four games and went 2-2 before Rodgers returned for the regular-season finale against the Chicago Bears -- a game the Packers won to clinch the NFC North title.
Flynn completed 61.4 percent of his passes for the Packers last season while throwing for 1,146 yards with seven touchdowns and four interceptions. He had returned to the Packers on a one-year, minimum-salary contract. Terms of his new deal were not released.
He left the Packers in free agency after the 2011 season and signed a three-year, $26 million deal with the Seattle Seahawks but failed to beat out then-rookie Russell Wilson for the starting job. A year later, he was traded to the Oakland Raiders and did not last a full season there.
Flynn is expected to compete with Tolzien for the backup job this season, but coach Mike McCarthy said last month at the owners meetings that he would like to keep three quarterbacks on the roster to open the season, something he hasn't done since Flynn's rookie year.
"Do I like Matt Flynn in the quarterback room?" McCarthy said last month. "Absolutely. Not only Matt as a player, but there's value he has, he's been there, he's got experience, his relationship with Aaron. He carries a lot of value. That's added value. But also you have to continue to improve. How do you improve? Competition."