Manager Lee Clark told the club website: "It's a massive blow for Nathan, his family and for the club.
"Nathan will be out for a period of time - we think we are looking at something like ten weeks."
Clarke made 24 appearances for Huddersfield last season, scoring three goals.
He joins his brother Tom on the sidelines, who is expected to be out of action until at least Christmas.
Clark added: "It's strange that the three long-term injuries we are dealing with in the squad at the moment for Nathan, Tom, and Lee Novak are the result of impacts.
"To be fair, Lee Novak is making decent progress in his rehab and things are going well for him, providing he doesn't suffer any adverse reactions.
In January we should know whether all three are going to be Huddersfield Town players or not
Lee Clark
"We'll take our time, though, because there's no sense in rushing him back. It's important we do things correctly, especially with it being pre-season."
Meanwhile, youngsters Jack Hunt and Lewis Franks have been allowed to go out on loan until January.
Hunt, 19, has joined League Two Chesterfield, while Franks, also 19, has gone to Oxford United.
Clark said: "Getting the young professionals out on loan is something I've always wanted to do. They need to be out playing at a good level where winning matters.
"At reserve-team level the result isn't always the important thing but now it will be very important.
"It's important that I see the lads in this environment and we will be going to watch them on a regular basis to compile dossiers on them.
"In January we should know whether all three are going to be Huddersfield Town players or not."
Source: BBC Sport
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