The girl is the second teen in Darwin to face such charges within a week after a 15-year-old boy faced the Northern Territory's youth justice court on October 29.
Neither teen can be legally identified due to their age.
The girl appeared in court on Wednesday, charged by the Joint Counter Terrorism Team NT with collecting or making documents likely to facilitate terrorist acts.
The charge carries a maximum sentence of 10 years in jail.
The boy, her alleged conspirator, was charged with possessing and sharing extremist material.
The charges against both teens followed a joint investigation by Australian Federal Police, NT Police and the Australian Security Intelligence Organisation.
It's alleged the teens had a "mixed ideological motivation", both posting content online that glorified mass casualty attacks on schools and places of worship.
Judge Giles O'Brien-Hartcher said the girl's texts to the boy were "extremely concerning" and allegedly showed she had attempted to break into her family's gun safe but had failed to do so.
On Tuesday, police executed a search warrant at the girl's Darwin home, where they seized clothing, documents, electronic devices and controlled and alleged prohibited weapons.
Defence lawyer Brooke Houen said she was seeking an adjournment for a bail application, and asked for an assessment of the girl for electronic monitoring.
The teen wept as she saw family members sitting in the court on Wednesday.
Mr O'Brien-Hartcher adjourned the matter to November 13 for the bail application.
AFP Commissioner Krissy Barrett said on Wednesday youth radicalisation might be the greatest challenge Australia faced.
''In the current climate of fraying social harmony, we are seeing more disengaged, confused, resentful and sometimes violent young people," she said.
"Some young people, impressionable and curious, are just being manipulated, and a lot of the time, it's via social media."Â
Ms Barrett said the number of young people counter-terrorism teams were investigating was increasing and addressing the issue required a whole-of-society effort.
NT Police Commissioner Martin Dole said the identification of a second young person during the investigation was deeply concerning.
''These are serious allegations and they reinforce why we cannot afford to be complacent about violent extremism or the influences young people can encounter online," he said.
Mr Dole said people should be alert but not alarmed.
"If something concerns you, tell someone,'' he said.
"Information from the community can make an enormous difference.''
NT Chief Minister Lia Finocchiaro said criminal intelligence sharing was one of the most powerful ways to combat terrorism.
"These investigations prove the strength of the system and Territorians can continue to have full confidence in it to keep us safe," she said.
