Sanatan Thakur, a resident of Purulia, was arrested from Renukoot on Sunday night. He was hiding in a temple disguised as a monk, Superintendent of Police from Purulia Joy Biswas told IANS.
The officer said the accused would be brought back to West Bengal. Mr Thakur was missing since the incident came to light on July 15.
After the child died, the police arrested her mother for allegedly aiding him in the crime.
"Thakur is slapped with charges of rape (IPC 376), murder (IPC 302), criminal conspiracy (IPC 120 b) and various sections of Protection of Children From Sexual Offences (POCSO) Act," the officer added.
The girl child was admitted to state-run Seth Sukhlal Karnani Memorial Hospital on July 15. While the mother of the child only complained about fever, the doctors found that as many as seven needles were pierced into the child's body and one of her arm was also broken.
The doctors performed a surgery to take out all the needles from her body but failed to save her as she succumbed to sepsis and pneumonia on July 21.