"We had Leighton's ankle checked. He has had surgery. It was straight-forward. He will be out until the start of pre-season," Everton boss Roberto Martinez said at a news conference on Thursday.
"We have found the solution. His time out will now allow him to be refreshed."
Baines, who started in England's 4-0 win over Lithuania in March, was injured during Everton's defeat by Sunderland last weekend.
Everton, who are away to West Ham United on Saturday, are 11th in the Premier League but have an outside chance of qualifying for the Europa League through UEFA's Fair Play system and Martinez, unlike some managers, would welcome it.
"I would welcome whatever comes our way. If it is earlier rounds in the Europa League, it would be a great opportunity and a good challenge for the youngsters to be involved in the early rounds," Martinez said.
"It would be a chance to show the good work we are doing behind the scenes."
(Reporting by Martyn Herman. Editing by Patrick Johnston)
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