Goodell, 52, has been commissioner of the NFL since 2006 when he replaced Paul Tagliabue. He is credited with helping the league negotiate a 10-year collective bargaining agreement with the players' union that ended last summer's labor lockout.
His new agreement runs to March 31, 2019.
"I speak on behalf of 32 NFL club owners in saying we are fortunate to have Roger Goodell as our commissioner," said Atlanta Falcons owner and Chairman Arthur M. Blank, who serves as chairman of the NFL Compensation Committee.
"Since becoming commissioner in 2006, the NFL -- already the leader in professional sports -- has gotten even stronger. As evidenced by this contract extension, we have great confidence in Roger's vision and leadership of the NFL. Our clubs, players and fans could not ask for a better CEO."
Among issues Goodell has faced while commissioner are player health and safety, retired players' medical needs and pensions, personnel conduct and international development.
"It is a privilege for me to serve the NFL," said Goodell. "It is the only place I have ever wanted to work."
Goodell first worked in the NFL office in 1982 when he was an administrative intern to Commissioner Pete Rozelle. Among his later assignments were positions as executive vice president and chief operating officer.