The London borough of Westminster has launched an inquiry into how the offender, who had been a known danger for five years, was not identified to the school as a threat.
The boy, who cannot be named, attacked the 28-year-old as she was marking books alone in her classroom after lessons. It was her second day in the post.
He threatened to kill her several times, biting her on the breast, headbutting her and pulling off her trousers and underwear. The struggle went on for about 12 minutes before he forced her to engage in oral sex.
The teacher, who also cannot be identified, has been unable to return to work.
It emerged this week that the boy had been excluded from primary school at 10 following attacks on pupils. His headteacher had warned social services about his behaviour. However, the boy's trail of offences was masked because he attended several schools in different boroughs.
A report on him, following the primary exclusion, said he felt rejected by not knowing his father. He was apparently bullied while living in a homeless hostel with his mother.
Under the Children Act schools, social services, police and other agencies should work in partnership and share information.
But John Dunford, general secretary of the Secondary Heads Association, said the lessons of Soham had not been learned.
"Again we have a violent attack by a known trouble-maker, but the school is unaware of his history. Unfortunately the information flow between schools and other agencies still seems to be one-way traffic. I can see no justification for not warning a head there may be a problem on the premises."
A Metropolitan police spokeswoman said: "We are working closely with our partners to see what lessons can be learned and looking to find out when this individual came to police notice."
The head at the victim's school said: "We regard this abhorrent crime as a completely unacceptable, but isolated, incident."
The teenager, who admitted the rape, had been in trouble with police three times during a six-month period before the offence. He was remanded in custody for reports and will be sentenced on June 17.