Faulkner, whose brilliant unbeaten 69 lifted Australia to an unlikely victory over England in the second one-day international in Brisbane this month, will also miss the Test tour of South Africa.
"James injured his knee during the Australia Day one-day international in Adelaide," Australia physiotherapist Alex Kountouris said in a Cricket Australia statement.
"He has had subsequent scans and was reviewed by Cricket Australia's medical team and a knee specialist, and will require arthroscopic surgery on Tuesday.
"He will not be available for the upcoming Test tour of South Africa. We are hopeful that he will recover in time to play the Twenty 20 games on that tour and take part in the ICC World Twenty20."