A statement from the England and Wales Cricket Board (ECB) said Flintoff had keyhole surgery in the Netherlands and would undergo a period of rest and convalescence.
"Following discussions between the ECB medical team, the England selectors and Flintoff, it has been decided that the priority will be for him to regain full fitness ahead of England's home international programme in 2008," the ECB said.
The operation removed extra bone and bone fragments from the back and front of Flintoff's ankle which were causing compression of the tendon.
"The surgery was performed successfully and, at this stage, the surgeon is optimistic that he has addressed the underlying root of the problem," the statement said.
Flintoff, who also had surgery earlier this year, will miss the forthcoming Test series in Sri Lanka and is considered "unlikely" to tour New Zealand.
