She died in the evening, Hospital Superintendent Shyama Kanungo said.
The body would be handed over to the victim's family in the presence of police personnel following a post-mortem, she added.
The girl was rescued in a critical condition from a school campus in Jagannathpur village under the Salepur police station on the evening of April 21. She had deep injuries on her head, face, neck and in her private parts.
The village is located at a distance of about 30 km from Cuttack.
A 25-year-old man of the village was arrested in connection with the incident on April 22 and remanded to judicial custody on charges of rape and attempt to murder under the Protection of Children from Sexual Offences (POCSO) Act.
"Since the victim has died, the attempt to murder charge will be converted to murder charge," Salepur police inspector DK Mallick said.
A 13-member team of senior doctors was attending to the victim, who was kept in the ICU, the hospital superintendent said.
All possible treatment available here was provided to her, Ms Kanungo said, adding that her condition started deteriorating further from Thursday.
Since her condition was not stable during the last 72 hours, it was not possible to shift her to a better facility, the doctors treating the girl said.
On the evening of April 22, the girl had gone to a shop in the village to buy biscuits. When she did not return after a while, the family members had launched a search.
She was finally found inside the school campus in an unconscious state, with no clothes on her body and blood oozing out of her head and mouth.
She was taken to a private nursing home nearby and later, shifted to the SCB Medical College and Hospital.
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