The incident took place last evening when the girl was alone in the house at Nabapally as her parents had gone to a doctor with her elder sister.
Taking advantage of the situation, their 27-year-old neighbour, who was a frequent visitor, entered the house and committed the crime, SP Kunal Agarwal said.
Alerted by barking of dogs, her family members found her lying in a pool of blood behind their dwelling unit.
She was declared dead after she was taken to hospital.
The youth was arrested today, the SP said.