The contract has a base value of $9 million and maximum value of $14 million, according to a league source.
Clayborn, 27, generated interest in free agency, including from the Dallas Cowboys, but Falcons coach Dan Quinn said all along he wanted to keep Clayborn in the fold.
Quinn said his focus was on improving the offensive and defensive lines. The signings of Clayborn and former Miami Dolphins defensive end Derrick Shelby helped bolster the line on the defensive side of the ball. Earlier in the day, the Falcons and three-time Pro Bowl center Alex Mack agreed to terms on a five-year contract.
Clayborn, a former first-round pick of the Tampa Bay Buccaneers in 2011, showed flashes in his first season with the Falcons last year. He was second on the team with three sacks and led the team with 15 quarterback hits.
Clayborn showed the versatility to play inside and on the edge, although the coaching staff realized he should have remained at defensive end for the duration of the season.
Clayborn also had 15 combined tackles, four tackles for losses and a fumble recovery.
Last offseason, the Falcons signed Clayborn to a one-year, $3 million "prove it" deal in light of his injury history. He did not miss a game in 2015 after being put on injured reserve in September 2014 with a right biceps tear.
ESPN Falcons reporter Vaughn McClure contributed to this report.