Janai Safar, 32, was arrested after arriving in Australia with a group of women and children who were all returning from a Syrian refugee camp on Thursday night.
Donning prison greens and a white hijab, she faced a NSW Bail Division Court on Friday via audiovisual link charged with entering a prohibited area and being a member of a terrorist organisation.
Both charges carry a maximum sentence of 10 years in prison.
Her lawyer said an issue in the case will be how heavily involved she was with the terror group and whether she was pressured to go along with their activities.
Michael Ainsworth also noted the alleged offending occurred years ago and she was unlikely to reoffend.
"March 2017 is when she effectively leaves Raqqa, which mean's she's no longer in the declared zone and certainly no longer declared to be a participant of the organisation," Mr Ainsworth told the court.
"We're looking at charges that are now effectively nine years old and offences alleged to be committed by her 12 years ago."
But Judge Daniel Covington ruled she did not meet the exceptional circumstances needed to be granted bail despite her nine-year-old son having never lived away from her.
"The factors have some strength, on the other hand I can't lose sight of ... the serious nature of the charges," Judge Covington said when denying bail.
Her case will return to court on July 15.
Safar was one of three people charged following an almost decade-long investigation which began after the women travelled to the Middle East with their partners, who intended to fight for Islamic State.
Kawsar Ahmad, 53, also known as Abbas, and Zeinab Ahmad, 31, faced Melbourne Magistrates Court on Friday morning charged with several crimes against humanity offences allegedly committed in Syria.
In a packed courtroom, the women appeared separately along with supporters.
The elder woman appeared first wearing a light brown hijab, before the younger woman was led in afterwards wearing a black hijab.
They were both remanded in custody until Monday when they will apply for bail.
Detectives allege the 53-year-old travelled to the region with her husband and children in 2014 and was complicit in the purchase of a female slave for $US10,000, and knowingly kept the woman in her home.
It is alleged the younger woman also had knowingly kept a female slave in her Syrian home in 2014.
Police said the pair were detained by Kurdish forces in 2019 and held with other family members in Al Roj Internally Displaced Persons camp.
AFP Assistant Commissioner Counter Terrorism Stephen Nutt said operational planning for the potential return of individuals from the Middle East started in 2015 but the investigation remained active.
A senior AFP officer would not answer questions on Thursday about the fate of the children, many of whom were born in Middle Eastern prison camps notorious for squalid conditions and the presence of extremist groups.
But they are expected to need significant support to help them adjust to life in Australia and to determine whether they've been radicalised while overseas.
Some of the women travelled willingly to support their partners who wanted to fight for Islamic State, but advocates for the group say others were coerced or only went to the Middle East to keep their family together.
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