The girl, studying in class X at a state-run residential school for girls, had delivered a baby boy in the early hours at the school hostel on Tuesday.
However, the panic-stricken girl threw the newborn from the window of the hostel toilet, police said, adding that the infant died while undergoing treatment.
"During the preliminary investigation, it was found that the girl's marriage was fixed with her aunt's son. When she had gone to her house at Pitlam mandal during the vacations last year, they had physical relations which resulted in her pregnancy," a senior police officer said.
"The girl subsequently returned to the hostel and used to tell her teachers that she was unwell. However, she kept mum about her pregnancy and used to cover her stomach. Apparently, the nursing staff who used to conduct health check up also failed to notice it," the officer said.
Police have registered a case under Section 315 of IPC (act done with intent to prevent child being born alive or to cause it to die after birth) against the girl, who has been shifted to a hospital for treatment.
A case of rape has been booked against the her aunt's son and efforts were on to nab him, police added.