The accused Jaffer, who is absconding, took the minor girl in his auto-rickshaw to an isolated place on June 29 noon and allegedly raped her, Rajendra Nagar police station sub-inspector K Kanakaiah said, based on a complaint lodged by the girl's mother.
After the complaint, a case was booked under relevant sections of the Indian Penal Code and the POCSO Act, he said.
The girl was sent for medical tests.
Efforts are on to nab the auto driver and a probe is on, he said.