Staff at the state secondary school in Salford, Greater Manchester, discussed the termination with the teenager, made sure she was comfortable with her decision and gave her time off to have the procedure.
It is understood the distraught teenager had gone to a hospital where doctors confirmed she was pregnant. Following her wishes, they didn't tell her parents but did notify the school.
The law states that teachers, doctors and nurses can offer sexual advice or treatment - including an abortion - to children without telling their parents as long as the child is considered mature enough to make the decision.
In the Salford case, it is believed the girl didn't want her parents to know because she was embarrassed and ashamed.
She eventually told her parents, but only after the abortion had been carried out.
The school, which has not been named for legal reasons, declined to comment on the case.
Councillor John Merry, assistant mayor for services for children and young people at Salford council, said: "There are very clear and stringent national guidelines for schools to follow in these situations.
"These guidelines are there in the best interests of the child and were followed correctly in these circumstances."
The law protecting teachers against charges of aiding and abetting a child sex offence is governed by a House of Lords ruling in the case of Victoria Gillick from 1985.
She took her local authority and the Department of Health to court in an attempt to stop doctors from giving contraceptive advice or treatment to under 16-year-olds without parental consent.
But the final ruling went against her and law lords said children could give consent and receive treatment if they understood the consequences, could not be persuaded to inform their parents and were likely to begin or continue having sexual intercourse with or without contraceptives.
It is illegal for anyone under the age of 16 to have sex - and the punishment is up to five years in prison. But it is 'highly unlikely' that children of the same age would be prosecuted, providing the activity was consensual and there was no abuse or exploitation, according to Crown Prosecution Service guidelines.
Teachers, doctors and nurses do not commit an offence of aiding or abetting a child sex offence if they give help in order to protect them, prevent them from pregnancy or sexually transmitted infection or do it to promote their emotional well-being.
There is no need to have parental consent to give advice or treatment, which can include an abortion, if the child is considered to have the maturity to make their own decision. Consent from parents is not legally necessary because youngsters are entitled to confidentiality. This can only be broken if their health, safety or welfare is considered to be at risk.
He said: "There is a clear route that all women, including young women, must go through if they want to have an abortion.
"Schools have a vital role in ensuring young people know about, and can access, sexual health services when required.
"It is right that a young person faced with an unplanned pregnancy has access to the information, support and space they need to make and act on decisions in a timely way."
However, Michaela Aston, senior education officer for pro-life charity LIFE and a teacher for over 25 years, said it was a 'time to worry' when schools were going behind the backs of parents.
He said: "When parents leave their children at the school door, they have an implicit trust that this institution will act in the best interest of their children without leaving them out of the equation.
"The school is being complicit in covering up and indeed contributing to a major, controversial and potentially-damaging event in the life of someone's daughter."