The money was donated to Echuca Twin Rivers School, Echuca Specialist School and River City Christian College in $3000 cheques.
"The funds for the Koori Kids Engagement Program will incorporate scholarships for about 30 Aboriginal children in Echuca," Njernda chief executive Aaron Wallace said.
"The money will be used for uniforms, in-class tutoring and support with excursions, so kids will be able to go on excursions they probably couldn't afford otherwise."
Mr Wallace said Njernda hoped to build a stronger partnership with schools in the community.
"We want to let them know Njernda is here to help resource the community and support our Aboriginal children," he said.
Schools across the region applied for the $3000 cheques and nominated students for the scholarships.
Twin Rivers social worker Emily Flanigan said she was delighted the school was among those selected for the donation.
"We're incredibly grateful as a school, this kind of money doesn't come to schools easily," she said.
"It's really nice to have a partnership with such a great organisation in our community that works with indigenous students and families.
"We're still thinking about how we'll use this money but are looking at providing extra support on site for our Koori students, looking at better resourcing around students to better incorporate culture into our curriculum.
"Above all, we're really excited about the opportunities this brings."