The incident occurred on Sunday when the girl was alone at her home. The matter came to light when the victim narrated the incident to her mother after which a complaint was lodged, Sub-divisional police officer Kedar Kumar Sahoo said.
The boy, arrested yesterday from his relative's house in Bhadrak, is a plus-two student.
Both the girl and the accused were medically examined, he said.
The boy was produced in the Juvenile Justice Board which remanded him to a reformatory home in Angul.