The Ulster and Ireland flanker suffered the injury on provincial duty in November, but had been expected to be back in action at some point during the RBS 6 Nations.
However, the 27-year-old has had to undergo another procedure to clean out bone fragments and will be absent until late May or early June, just as the British & Irish Lions embark on their tour of Australia.
An Ulster statement read: "Ulster back-row forward, Stephen Ferris, was reviewed last week as part of his ongoing rehabilitation from an ankle injury that he sustained in November.
"At that review, it was discovered that although he had made excellent progress, some minor issues still remained.
"Those issues included function at the ankle continuing to cause pain.
"Having considered all specialist medical opinions given, Stephen underwent successful ankle surgery in Belfast yesterday (Wednesday), during which fragments of bone were removed.
"Stephen will be out of rugby for a further three months but following this period is expected to make a full and complete return to the game."
Ferris was also unfortunate with injury on the Lions' 2009 tour of South Africa.
The back-rower had appeared set for a place in the Test side after a series of impressive displays, only for a knee injury to end his trip prematurely.
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