The alleged assault occurred in the small community of Ali Curung, 170 kilometers south-east of Tennant Creek.
Northern Territory police previously confirmed the Northern Territory Child Abuse Taskforce were investigating the alleged sexual assault and also confirmed that a teenager had been taken into police custody and was assisting with the investigation.
Today a police spokesperson confirmed the charges.
"A 16-year-old male has been charged with sexual intercourse without consent and will appear in Alice Springs Youth Court today."
NT Chief Minister, Michael Gunner said he is aware of the incident.
"This is an extremely disturbing incident. Every child, no matter where they live, deserves to be in a safe environment."
Mr Gunner said additional staff from Territory Families had been deployed to the community, and the matter would be referred to the Children's Commissioner for investigation.