Adam Brookman, 39, says he was carrying out humanitarian work in Syria when he was forced to work with Islamic State (IS) militants.
He was detained at Sydney airport on Friday after surrendering to officials in Turkey.
Mr Brookman has been charged under new anti-terror laws with knowingly providing support to IS.
The offence carries a maximum sentence of 25 years in prison.
He also faces a second charge of "performing services with the intention of supporting a person, or persons, to engage in a hostile activity in a foreign state".
The nurse made no application for bail when he appeared briefly at Melbourne Magistrates' Court. He was remanded in custody pending a hearing on Monday.
Police said that although there was no evidence that Mr Brookman posed a threat, they had acted to protect the community.
Mr Brookman, a Muslim convert, has told Australian media that he travelled to Syria to do humanitarian work but was forced to work with IS when he was injured in an air strike and taken to a militant-controlled hospital.
His return to Australia had been negotiated with Australian government and international agencies, police said.
New Foreign Fighters legislation has made it a crime to assist militant groups in the Middle East.
Australia is on high alert for attacks by radicalised Muslims, including those returning home from fighting in the Middle East.
In December last year, the country specifically banned travel to Syria's Raqqa province, which is held by IS.
It means anyone entering the area could face up to 10 years in prison unless they have a legitimate reason, including family visits, journalism or aid work.
According to the government, at least 100 Australians are fighting with terror groups in the Middle East, and another 150 people in Australia are known to be supporting such groups.
A nurse has been charged with terrorism offences after he voluntarily returned to Australia from Turkey.