The alleged crime came to light when the girl was found to be pregnant and carrying a dead foetus, police said.
She told her mother that a boy in the neighbourhood, who used to stalk her, took her to his house forcibly some ten months ago and raped her.
The girl, however, continued to meet him and had a sexual relationship with her.
Her mother approached Bhavani Nagar police with a complaint of rape last week.
During the probe, the girl told police that two other boys had raped her too, said Assistant Commissioner of Police Mohd Tajuddin Ahmed.
Police took all three boys in custody, the ACP said, adding they “admitted the guilt”.
A case of rape under the IPC and relevant sections of the Protection of Children from Sexual Offences Act has been registered and further probe is on, he said.