The team said Wednesday that he'll have the operation Thursday in Los Angeles.
The Oilers didn't provide a timeline for his return, saying only that he's "out indefinitely," but Khabibulin's agent, Jay Grossman, said the goalie will need 12 weeks to recover from surgery.
That leaves him a narrow window to try and return during the regular season.
Khabibulin hasn't played since a 3-2 shootout loss to Columbus on Nov. 16. He has a 7-9-2 record with a 3.03 goals-against average and a .910 save percentage this season.
The 37-year-old signed a $15-million, four-year contract with Edmonton during the summer.