No money figures were released, but the Atlanta Journal-Constitution reported Kovalchuk ended his holdout with a deal worth $30 million over five years.
"Ilya is an important part of our franchise and we share in our fans excitement that he is back with us for many seasons to come," said General Manager Don Waddell. "He is one of the league's elite players and will play an integral part in helping us take that next step."
Kovalchuk, 22, tied for the NHL lead with 41 goals in 2003-04 after being chosen first overall by the Thrashers at the 2001 NHL Entry Draft. His 87 total points that year tied for second in the league.
He has 108 goals and 205 points with 46 multiple-point games, 70 power-play points, 32 power-play goals, 133 even-strength points and 75 even strength goals in 227 games.