Cutler, 30, just completed his eighth NFL season. He played in 11 games, missing five due to injury, in which the Bears went 5-6.
Cutler could have become an unrestricted free agent but the new agreement links him to Chicago through the 2020 season, Bears General Manager Phil Emery said. Financial terms of the new deal weren't released.
"We're very excited to have Jay for the long term. He battled through the tough times and kept fighting," Emery said.
Cutler played his first three NFL seasons with the Denver Broncos before joining the Bears for the 2009 season. In the five seasons since, he has become the team's record holder with 1,258 completions, 14,913 yards and an 83.1 quarterback rating.
Cutler completed 224-of-355 passes for 2,621 yards with 19 touchdowns and 12 interceptions in the just-ended season.
The Bears also said they signed cornerback Tim Jennings and guard Matt Slauson to four-year contracts. Like Cutler, Jennings and Slauson could have been unrestricted free agents.