Cisse limped out of the 2-1 defeat to Swansea City on April 19, and has not featured since for Alan Pardew's men.
The Senegalese striker has endured a torrid campaign, with just two goals to his name in 24 Premier League appearances.
On Friday, the club issued a statement confirming that the forward had undergone the procedure and would be out for some time.
"Newcastle United can confirm that striker Papiss Cisse underwent an operation on a fractured patella on Thursday," it read.
"Cisse, aged 28, will spend his rehabilitation period at the Clairefontaine Medical Centre before returning to Tyneside to be further assessed by the club's medical staff.
"He is expected to be sidelined for a number of months."
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