The girl had come home from school on Wednesday during the lunch break for a quick bite, according to news agency Press Trust of India. She returned to the primary school after having her meal.
This was the last that her family had seen of her.
When she did not return from the village school till late in the evening, her mother went around looking for her and later reported complained to the police that her daughter was missing.
The local police spoke to people along the route that she had taken to school. It turned out that someone had seen the girl with villager, 22-year-old Shiva Kumar. According to reports in local media, he was the girl's uncle.
Shiva Kumar was arrested on Thursday morning.
"The girl, who goes to a nearby primary school, was raped and murdered by the accused in Mannapur village in Mogdampally mandal," N Ravi, a senior police officer of Telangana's Sangareddy district said, according to PTI.
Shiva Kumar is alleged to have told the police that he had taken the girl to a nearby farmland and raped her, twice. Mr Ravi said he also told them that he had thrown the girl into the nearby well. The girl's body was pulled out from the well soon after.