Jenkins finished the 2002 season with 60 tackles and 7 sacks, en route to an alternate appearance on the NFC's Pro Bowl team, where he replaced an injured Warren Sapp. The following season, he helped the Panthers on their way to Super Bowl XXXVIII. In one game against the Tampa Bay Buccaneers, Jenkins blocked two kicks: a field goal attempt by Martin Gramatica, and an extra point attempt that would have won the game. Jenkins' second block marked the first time that an extra point was blocked to send a game into overtime (Carolina later won the game). Jenkins was rewarded with his first Pro Bowl start, and joined teammate Mike Rucker as half of the NFC's defensive front line.
On February 29, 2008, the Carolina Panthers traded Jenkins to the New York Jets for third- and fifth-round draft picks in the 2008 NFL Draft. For much of his first season with the Jets, Jenkins was dominant and garnered heavy consideration for the NFL's Defensive Player of the Year award. On Sunday October 18, 2009, Jenkins left the game against the Buffalo Bills with a left knee injury. The next day, it was reported that he had a torn ACL and would be out for the rest of the season. During the home opener against the Baltimore Ravens on September 13, 2010, Jenkins was injured as he twisted his leg making a tackle. A few days later, an MRI revealed that Jenkins had again tore his ACL, in which he was eliminated for the rest of the 2010 season.
The Jets released Jenkins on February 28, 2011.
Prior to the 2011 NFL Season, Jenkins joined SNY as an analyst for New York Jets games, even though he is likely best remembered as a Panther. His job includes appearing on Jets programs such as pre-game and post-game shows and Jets Game Plan.