Rafinha last played for Barcelona in their 4-1 victory over Granada on Sunday.
The Brazilian started the match but was replaced on 17 minutes after injuring his right knee.
Barcelona confirmed at the time he’d suffered an injury to his meniscus and following surgery he will now miss the crucial run-in to the end of the La Liga season.
Rafinha will be sidelined for four months
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A statement on the club’s website read: "At midday on Friday local time the first team player Rafinha underwent arthroscopic surgery on his right knee to resolve an injury to the internal meniscus.
"The operation was carried out by Dr.Ramon Cugat and Dr.Ricard Pruna. The player will be out for around four months."
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Barcelona will be without Rafinha for the final few games of the season
Rafinha has notched up seven goals in 28 games for the Catalan giants this season.
The news will come as a blow to Luis Enrique with his side trailing Real Madrid by two points.
Real also have a game in hand on their rivals with both teams set to met at the Bernabeu on April 23.