The Gunnedah and Tamworth Girls Academy program has been saved after fears it would be forced to close when the national organisation lost all its funding in a shock decision just before Christmas.
There are academies in a number of local high schools, including Tamworth and Gunnedah High Schools.
Local advocates were concerned that both faced closure after the December 22 announcement that parent charity Role Models and Leaders Australia Limited would no longer get any federal government funding in the new year.
The organisation had provided in-school support and mentoring for Indigenous girls for 16 years.
In a statement on Thursday, peak funding organisation the National Indigenous Australians Agency announced that a new organisation had won an open tender to provide the service.
The Redfern-based National Aboriginal Sporting Chance Academy will provide the service at the Tamworth and Gunnedah High Schools from term one.
CEO Leanne Townsend said the institution was likely chosen because it has a track record of success, and is led by Indigenous people.
But Ms Townsend would not commit to maintaining employment of current at the schools' academies.
She said the organisation would aim to roll out a "participatory model" in partnership with young people and the community.
"I understand there is concerns with the change but there's also some positives that can come from change," she said.
"Because we're centred on the best interests of young people, our job is to support and to empower. So we're going to walk alongside these young women. I guess it's hard at this point to understand but I can certainly see that vision. There's no need to be fearful."
Despite their name, the Sporting Chance Academy is not exclusively a sporting organisation.
Ms Townsend, who is Indigenous, grew up in Uralla.
"I've been debating in Gunnedah High School when I was in year 7," she said.
"I went all the way through school up there!"
She said the charity would aim to use their new local base to expand not-for-profit services throughout the New England.
Minister for Indigenous Australians Ken Wyatt announced in December that the government would spend $36 million over three years expanding the girls academy program.
Some 2,900 students participate in the program at 46 locations across Australia.
The program is designed to increase Year 12 completion rates, and can include everything from group homework sessions to health check-ups and school transport.
The National Indigenous Australians Agency recently ran an open and competitive grants process for the program's tender.
The Oxley High School's Girls Academy has closed and is not included in the funding round.