The Class VII student, hailing from Thathankulam near Tuticorin, used to go to the private school near Nazareth by local train and was reported missing on Thursday after she did not return home.
Her body was found in a bush near the railway level crossing at Syedunganallur, about 30 km from Tuticorin, on Friday morning, police said, adding she had been raped before being murdered.
Police said investigations were on to nab the culprits.