Samiullah was arrested from Chhitauni bus stand in Motihari town and raids are being conducted to nab four others accused in the case, Jitendra Rana, SP East Champaran district said.
The four others include the Samiullah's father and three brothers.
The girl in her complaint had alleged that her neighbour Samiullah had raped her on June 13 at Jamai Tola village of East Champaran district.
She informed her mother of the incident and lodged a complaint on June 15.
The girl's mother claimed that when she went to the accused's house to complain about the incident, his family attacked her daughter and inflicted injuries to her private parts.
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The girl's father has claimed that her medical report has been changed with the connivance of the police.
A woman investigation officer was appointed for the case on June 22, a release from the Director General of Police (DGP) said.
Police had also requested the court to record the victim's statement under section 164 of the CrPC, it added.
The SP said the girl has been provided protection at Motihari Sadar hospital where she was being treated, while her family too has been provided security cover.