The school was closed while police carried out forensic examinations after the alleged attack on the teacher last Tuesday.
The boy faced rape and sexual assault charges at Inner London Youth Court on Friday and was remanded in custody. He is due at the same court this Friday.
The local council said it was giving staff at the school support.
A council spokesman said: "The local education authority is offering support and guidance to the head teacher and staff.
"The school regards this as an unacceptable, but isolated incident."
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