39-year-old Adam Brookman has been charged with one count of knowingly providing support to a terrorist organisation.
He was extradited to Victoria last night after being arrested at Sydney International Airport on Friday.
Mr Brookman claims he travelled to Syria to carry out humanitarian work, and was forced to work for IS.
He did not apply for bail, and is due to face the Melbourne magistrates court again tomorrow.
A warrant for Brookman's arrest on two terrorism-related charges was issued on Friday.
Court documents outline one charge relates to Brookman knowingly providing support to IS by undertaking guard duty and reconnaissance between April 2010 and August 2014.
It is alleged that support would help the group "prepare or foster" a terrorist act.
The second charge relates to undertaking the guard duty and reconnaissance with the intention of supporting IS.
Brookman has claimed to Fairfax Media he was in Syria for humanitarian work, but was forced to join the terrorist group after being injured and sent to IS-controlled territory.
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