The Peru international struggled with the complaint throughout the previous campaign, making just 19 Bundesliga appearances.
It was announced last week that a close-season of physiotherapy had failed to have the desired effect, and that Farfan would likely require surgery to address the issue.
On Monday, Schalke confirmed that the 29-year-old had gone under the knife, adding that the operation had been a success.
"Jefferson Farfan underwent successful knee surgery on Monday morning in Regensburg," read a message from the club's official Twitter account.
Farfan is now expected to miss the start of the new season, which gets under way next month.
Schalke begin the 2014-15 campaign with a visit to Hannover.
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