Nike, which signed Vick as a rookie in 2001, terminated his contract in August 2007 after he filed a plea agreement admitting his involvement in a dogfighting ring. Vick spent 21 months in prison.
CNBC first reported the deal. Terms were not released.
"Michael acknowledges his past mistakes," Nike said in a statement. "We do not condone those actions, but we support the positive changes he has made to better himself off the field."
Vick was voted The Associated Press Comeback Player of the Year after missing two seasons and playing sparingly in 2009.
"Michael is committed to working with Nike and wants to utilize his platform as a professional athlete to have a positive impact on our youth," said Andrew Stroth, the Chicago-based attorney who negotiated the deal for Vick.
Nike and Vick initially renewed their relationship in 2009, when the company announced it had "agreed to supply product" to the quarterback, who was not under contract. Nike has similar agreements with several athletes with whom it doesn't have endorsement deals.
Vick signed a one-year contract with the Eagles in March, a few weeks after being designated as the team's franchise player. He led the Eagles to a 10-6 record and the NFC East title after replacing an injured Kevin Kolb in Week 1.
Despite missing three games with an injury, Vick re-established himself as one of the most exciting players in the NFL. He set career highs with 3,018 yards passing, 21 touchdown passes, nine touchdowns rushing, a 62.6 completion percentage and a 100.2 passer rating.