The incident took place on Thursday at Purunapani village when the girl's parents were away from home, Deepak Kumar, suprentendent of police, Jajpur said.
The youth, also resident of the village, had allegedly threatened the 13-year-old girl with dire consequences if she reported the incident.
He was arrested last night after the girl's father lodged a complaint with the police.
Medical examinations were conducted on the accused and the victim.
The accused was produced before the court of the Judical Magistrate (First Class) at Jajpur road which remanded him to judicial custody after his bail application was rejected.
