The boy was found dead last Wednesday. The police were earlier probing if he had been sexually assaulted before the murder.
The two boys, aged 16 and 13, who were apprehended today were inmates of the same rescue home, police said, adding that they were detained after the autopsy report.
According to the report, that the boy had been throttled to death, Saidabad Police Station's inspector A Srinvasulu said.
The 16-year-old boy was accused of having sodomised the victim and later killing him with the help of the other boy after the victim said he would report the incident, the officer said.
A case under section 302 (murder), 377 (unnatural sex) as well as under the Protection of Children from Sexual Offences Act has been registered.