The Italian midfielder has been beset by fitness problems this season, making just four starts for Gus Poyet's side.
Giaccherini last featured in the FA Cup fourth round replay against Fulham earlier this month, but faces a battle to play any further part before the end of the 2014-15 campaign.
"Emanuele is going to be out for a while," Poyet told the club's official website.
"It is incredible that he had a big injury after the Burnley game and it took him a while to come back, and then when you think everything is good he had another knock in the same area on the same bone and now it is going to take a little bit longer.
"He is practically going to be out right until the end of the season which is unfortunate for us, but we wish him well and I want to say a full recovery - not a quick one - so that we can count on him next year.
"He was like a new player in pre-season.
"I was happily surprised and I was really thinking about somehow finding a place for him in the team, so that was my challenge.
"He showed it at the start of the season and when he came back it was a different way because it was from an injury, but at Fulham he also showed something special and then he got a kick.
"Let's say that it is a season to forget for Giaccherini, so we just need to make sure he feels perfect for next season."
