Ferguson was drafted by the New York Jets with the 4th overall pick of the 2006 NFL Draft. On July 26, 2006, Ferguson signed a five-year deal with the team. The deal was similar to the $35 million deal that 2005’s No. 4 pick, Cedric Benson, signed with the Chicago Bears. Designated as Jason Fabini's successor, Ferguson started every game at left tackle for the Jets since the beginning of the 2006 NFL season. On January 8, 2010, Miami Dolphins Tackle Jake Long withdrew from the 2010 Pro Bowl due to injuries and Ferguson was named as his replacement. He was invited to the 2011 Pro Bowl.