The pair were arrested Monday, December 1 and charged with alleged aggravated break and enter and destroy property by fire in company.
Both teenagers were granted strict conditional bail to appear before a children's court on Wednesday, December 10.
Overnight, the NSW Department of Education confirmed that 30 classrooms were destroyed in the blaze, which was reported to emergency services at 12.45am Saturday.
Firefighters from across the district battled strong winds to try and save as much of the school as they could.
Officers from Murray River Police District established a crime scene and commenced an investigation under Strike Force Soderblom.
Following inquiries, detectives arrested the two teens on Monday.
The news comes as students prepare for a new way of learning to finish out the school term.
Police have released the site to the Department of Education, which will make the area safe before students or staff can return.
The rebuilding of essential facilities will take considerable time, requiring temporary arrangements for students.
Years 7, 8 and 9 students will continue to learn from home today while appropriate facilities are secured and prepared.
Those unable to work from home will be accommodated by Deniliquin South School.
Year 10 students are attending a camp in Sydney all week, while Year 11 students will be accommodated at Deniliquin TAFE Community Connection Centre and taught by high school staff this week.
Support Unit students will begin classes at Edward Public School, taught by their regular staff.
In the latest information shared with parents via the Schoolbytes system, Deniliquin High School has said counselling and support services are available from Deniliquin South Public School’s learning and support offices for students affected by the fire.
Parents seeking additional support for their children can contact the school on 5881 1211.