Thomas, the team's longest-tenured player, had his 2011 season cut short after suffering a season-ending Achilles tendon injury in Week 4.
Financial terms weren't immediately available.
"Bryan has meant a lot to this organization over his 10 seasons and we are excited he will continue his career here," general manager Mike Tannenbaum said. "He is a versatile defender who is adept as a pass rusher and against the run. He understands the defense, allowing him to play a variety of roles for us."
Thomas, who turns 33 in June, is rehabbing from surgery, but told The Star-Ledger of Newark on Monday that he's "right on schedule" and hoped to re-sign with the Jets.
Thomas has played 10 seasons with the Jets, who drafted him in the first round in 2002. He has 32½ career sacks and, until last season, had missed only two games. Thomas is a solid run defender and the Jets' perimeter run defense struggled without him. The Jets never settled on a full-time replacement either, using a linebacker-by-committee approach after Thomas' injury.
The Jets will still likely look to add a pass-rushing linebacker in April's draft. They were thought to be interested in former Ravens linebacker Jarret Johnson, an old favorite of coach Rex Ryan from their years together in Baltimore. It's not clear if the re-signing of Thomas will preclude them from pursuing Johnson.
In a span of 24 hours, the Jets locked up two longtime defenders. On Monday, they finalized a three-year contract with nose tackle Sione Pouha. The deal is for $15 million and includes $9.5 million in guarantees, according to a league source.