Jones suffered the injury in training earlier this week and was sent for a scan which has confirmed he requires an extensive period of rehabilitation.
A statement issued by the club read: "Phil Jones has had surgery on a knee meniscus tear sustained in training that will require six to eight weeks' rehabilitation."
It is desperate news for the 20-year-old, who is yet to make an appearance this season.
After an extensive break following Euro 2012, Jones suffered a back injury that prevented him playing any part in pre-season.
He missed United's opening three Premier League games and the start of England's World Cup qualifying campaign, but Jones' return to training was supposed to be the prelude to his comeback.
The new PUMA evoSPEED 1.2 FG. A great new soccer cleat with classic look and first time for PUMA to be on the cleat.
The adidas Nitrocharge is the most talked about new cleat in years. It was released on May 15 and will take your pitch by storm.
The Juventus jersey for the 2013/14 was released earlier this week. Be the first to wear the colors of the Old Lady.
The Liverpool 2013/14 soccer jersey is available for pre-order. The Reds are eager to compete for silver next season.
One of the top soccer cleats for control the Nike CTR360 will not let you down on the field in tight spaces.
Chelsea won the Europa League on Wednesday. The Blues defeated Benfica 2-1 on injury time goal from Ivanovic.
adidas has added some color to the Predator line with this new colorway. Released on May 17. Be the first to own a pair.
Bayern Munich are kings of Germany and hope to be crowned kings of Europe at Wembley later this month!
Ajax has released their away soccer jersey for the 2013/14 season. Get in the Gear.
The push for more color on their cleats, adidas has added the infrared colorway to the adiZero f50 Line.