The deal will pay Khudobin $2 million for the 2014-15 season and $2.5 million in 2015-16.
"We are pleased to be able to keep Anton with the Hurricanes," general manager Jim Rutherford said. "He has played well this season and signing him helps solidify our team's goaltending situation."
Khudobin, 27, is 13-8-0 with a 2.17 goals-against average and .927 save percentage in 22 games this season.
He was named the NHL's First Star for January after matching a Hurricanes record for wins in a month (10) and registering a GAA of 2.19 and save percentage of .927 in 14 games.
Khudobin was chosen by the Minnesota Wild in the seventh round (No. 206) of the 2004 NHL Draft, and has an NHL record of 27-13-1 with a 2.11 GAA and .930 save percentage in 43 games with the Wild, Boston Bruins and Hurricanes.