The alleged incident occurred at Pakala Pallepalam on Monday. The girl, who complained of stomach pain on Tuesday night, was shifted to a hospital; her condition was stable, police said.
The girl used to watch TV at the accused's house. On Monday, he raped her when there was nobody else in the house, police said.
The victim's mother alleged that the boy's relatives warned her against going to the police.
Police, who would be sending the teenager for medical tests to determine his age, have registered a case under Protection of Children from Sexual Offences Act and under relevant sections of IPC.