The teenager allegedly attacked the teacher, who was on her second day in the post at a central London school, last Tuesday.
The Westminster school, which cannot be named to protect the identities of the teacher and the youth, was closed the following day while police carried out forensic examinations.
The pupil appeared at Inner London Youth Court last Friday charged with one count of rape and one count of sexual assault on or about September 7. He was remanded in custody to reappear in court today, police said.
In a joint statement, the school and Westminster council said: "A Westminster school was closed last Wednesday following an assault on a member of staff at the school on Tuesday. A 15-year-old male has been charged and the school was reopened on Thursday following the completion of police inquiries.
"The local authority is offering support and guidance to the headteacher and staff.
"The school regards this as an unacceptable, but isolated incident. Across Westminster relations between staff and pupils are good, as demonstrated by three years of improving teacher retention and increasing school standards."
David Hart, general secretary of the National Association of Head Teachers, said although assaults on teachers took place on a daily basis, heads could not be expected to prepare for such a serious attack as rape.
He said: "It is extremely difficult to guard against such a wholly exceptional incident, which is something you do not expect to happen."
Figures published by the Department for Education and Skills in July revealed around 10 pupils are excluded from school every day for assault.
During the 2003 summer term, 288 pupils were expelled for violence against teachers or other adults and another 336 excluded for assaulting children, said the DfES.