Frimpong limped off in the 24th minute of Wolves' 2-1 win at Loftus Road – and a scan has revealed the worst for the 20-year-old, who was on a season-long loan with the Molineux club.
Statements on both club websites confirmed the player will see specialists in London over the next few days before having surgery and starting a programme of rehabilitation.
The midfielder, who suffered the same injury to his left knee in 2010, had made an impressive start to his temporary spell at Wolves, catching the eye during his five appearances in gold and black.
Wolves' statement said: "Emmanuel is expected to be out for a number of months and will therefore miss the remainder of this season.
"Everyone at Wolves would like to thank the midfielder for his efforts whilst at the club and join Arsenal in wishing him a swift recovery."
Frimpong tweeted on Monday: "I wanna thank all the wolves fans for their support since I've been here and really Hope wolves stay up this season."