Nicholas Tee, a 51-year-old married father of two, will soon be known to pupils at Charterhouse School in Godalming, Surrey as Nicola Tee.
The master is yet to have surgery, but is on a course of hormone treatments
to prepare for an operation, which is likely to take place within the next two years.
In a letter to parents, the school's head teacher, Rev John Witheridge, said there were "no medical or pastoral reasons" why he should not continue to teach.
"As well as legal advice, the school has taken extensive specialist medical soundings," Rev Witheridge assured parents.
The legal obligations on the school were "unambiguous", he said.
The head also sent parents a paper written by an expert on transsexuality which stressed that the condition - known as gender dysphoria or gender identification disorder - had nothing to do with homosexuality or paedophilia.
The maths, physics and technology teacher has taught at the school for 13 years, but has been on sabbatical since September.
Marriage
A family friend said the teacher's wife had decided to continue their marriage of 27 years and the couple's grown-up son and daughter were supporting the sex change.
"Nick knew from when he was a boy onwards that this was what he felt," the friend said.
"He struggled all those years in silence. No-one else knew. He felt like a woman imprisoned in the body of a man."
The master said he had been fortunate to have had tremendous support from family and friends
"I am very pleased to be carrying on teaching, which is what I have always wanted to do," he said.
Nicholas Tee studied engineering at Balliol College, Oxford between 1968 and 1971.
He rowed for the university in four boat races and also for Great Britain in the coxless four at the World Rowing Championships in Nottingham in 1975.