The England and Toffees full-back went under the knife on Thursday to correct the problem he sustained in training on the eve of the Barclays Premier League campaign.
Everton confirmed that the injury had been repaired but that the 30-year-old now faces a lengthy period of rehabilitation before he can return to first-team action.
A statement on www.evertonfc.com read: " Left-back Leighton Baines has undergone a successful ankle operation but is set to be missing for the next 12 to 14 weeks."
Everton revealed just ahead of their Premier League opener against Watford on Saturday that Baines had injured his ankle in training.
It is the same ankle on which Baines had surgery in May, a procedure that forced him to miss the final two matches of last season.
Toffees boss Roberto Martinez said of Baines' setback after the 2-2 draw with Watford: ''We don't know how long he will be out for, but it has been a real disaster.
''We were preparing for the Watford game and in one incident in training, he blocks the ball and it hits him in exactly the same place where he had surgery a few months back.
''It was devastating, because he had worked so hard and looked stronger than ever - I don't think I had seen him looking as powerful and refreshed in the last two seasons
Then there was this big knock."
Baines could now miss over a dozen Premier League matches for Everton, including the Merseyside derby against Liverpool, as well as five England matches.
Roy Hodgson's men face San Marino, Switzerland, Estonia and Lithuania in September and October as part of their Euro 2016 qualifying campaign, while November 17's friendly against France could also come too soon for Baines.
Source : PA
Source: PA