The 19-year-old has been ruled out of action for two months, which means he will miss the opening clashes of the new Premiership season.
The news is a particular blow to Boro's plans, as Murphy was already pencilled in to fill the left back role - which would normally have been filled by French star Franck Queudrue, but he is suspended for the opening five games of the season.
Murphy is understood to have broken a bone in his right foot and is unlikely to play again until September.
Boro boss Steve McClaren has already lost key central defender Ugo Ehiogu to cruciate ligament damage, but he has adequate cover in that department with both Chris Riggott and Andrew Davies looking to start the campaign alongside captain Gareth Southgate.
McClaren is now likely to turn to veteran Colin Cooper - who is the natural choice and only real alternative to fill in for Murphy and Queudrue.
The Teessiders have been concentrating all their efforts in the transfer market on midfield and attack, but now McClaren may be forced to look for extra cover.
Australian international Tony Vidmar, who was released by Boro at the end of last season, may also be given a chance to return to the club.
