Anne Lakey, 53, won national recognition after overseeing the biggest improvement in GCSE results in the country.
The chief executive of the Durham Federation of Schools has been charged with eight sexual offences against a boy under 16.
Noelle Brockbank, senior Crown prosecutor at CPS North East, said: "I have today authorised Durham Constabulary to charge Anne Lakey, 53, with four counts of indecent assault on a boy under 16, two counts of gross indecency with a boy under 16 and two counts of inciting a boy under 16 to commit an act of gross indecency."
The offences were alleged to have taken place between April 1988 and May 1989.
She will appear before Consett Magistrates' Court on January 7.
The alleged victim was not a pupil at a school where she worked, it has emerged. The head has been suspended for the last 12 months.
The federation includes Durham Community Business College, in Ushaw Moor, and Fyndoune Community College, in Sacriston.