The case was registered on Friday after the 16-year-old girl told her mother about the incident, police said.
In a release, police said Ananthu was accused of raping the girl multiple times and threatening the girl that he would pour acid on her if she told anyone what he had done to her.
Police also said that there was already a case under the Protection of Children from Sexual Offences (POCSO) Act registered against him for allegedly molesting the same girl earlier.