Sources told ESPN's Dan Graziano that the five-year deal is worth $86 million, of which $36.75 million is guaranteed at signing, including a $15 million signing bonus. The contract, which averages $17.2 million per season, also includes an injury guarantee of $53.5 million.
The deadline to sign long-term deals was 4 p.m. ET Friday. The Jets announced the signing on Twitter at 4:33 p.m., after which the 26-year-old Wilkerson reacted.
Wilkerson's average per year $17.2 million is the highest in team history. His $36.75 million guarantee is second only to Darrelle Revis ($39 million).
Wilkerson, 26, received the Jets' non-exclusive franchise tag (worth $15,701,000) on March 1. He was allowed to negotiate with other teams but any club that signed him would have had to surrender two first-round picks to the Jets.
He was unhappy at the prospect of playing the season under the tag, saying he was undecided if he'd report to training camp. He told the New York Post last month that he felt unwanted by the team, and he skipped the team's offseason workouts and mandatory minicamp.
Early in the week, there wasn't much optimism that a deal would get done. On Wednesday night, the Jets e-mailed a proposal that intrigued Wilkerson's camp. They offered a five-year contract; Wilkerson had been seeking a six-year deal, but he was willing to consider five years the numbers made sense. Even then, an agreement didn't seem likely.
At 3:15 a.m. Friday, nearly 13 hours before the deadline, the Jets e-mailed a revised offer. That prompted a full day of negotiating. An agreement was reached only minutes before 4 p.m.
He made his first Pro Bowl last season after leading the Jets with 12 sacks, a career high. He broke his right leg (fibula) in the final game, requiring surgery a few days later -- a six-month rehab, according to team officials.
After being examined by Charlotte-based orthopedist Robert Anderson in mid-February, Wilkerson tweeted an update, saying he was ahead of schedule in his rehab.
The subplot to his successful career -- 36 sacks in five seasons -- has been an ongoing contract drama. Unhappy without a long-term deal, Wilkerson skipped the Jets' voluntary workouts last offseason. He reported to training camp, but informed the organization that he didn't want to negotiate once the regular season started.
Even with an artificial deadline, the two sides didn't come close to an agreement. Wilkerson played last season for $7 million, the amount of his predetermined, fifth-year option.
Wilkerson, a first-round pick in 2011, has been a starter since Day 1. Technically, he's a 3-4 defensive end, but he can play any position on the defensive line, adding to his value.
In 16 games last season, he recorded 64 tackles and two forced fumbles. He grew up in Linden, New Jersey, about 20 minutes from MetLife Stadium.
ESPN Jets reporter Rich Cimini contributed to this report.