Quakers have always seemed slightly at odds with society. Their silent meetings, their pacifism, their refusal to swear on oath, and their gentle but firm dissent against authority and formality in church and state have made them appear somewhat remote from the realities of life.

But as the retiring 60-year-old head of a Quaker school, Ian Small is convinced the “Quakerly” way of doing things is needed more than ever. As the term closes, Mr Small leaves his headteacher’s accommodation at Bootham, a co-educational independent boarding school in the heart of York - and his beloved views of York Minster - quietly satisfied that Quakerly principles are alive and well after his 16 years of headship in a thriving and over-subscribed school.

Bootham has an informal atmosphere. Uniform is minimal and for the lower years only. Pupils and staff (teachers, cleaners, cooks) are generally on first-name terms. It runs, says Mr Small, along Quaker principles that pupils and staff will be truthful and trustworthy; that conflict should always be rejected in favour of co-operation; that people should always consider they may be mistaken; that the individual must be respected and silence esteemed.

On the whole, says Mr Small, these principles are upheld at Bootham. Many of his pupils agree. “This is a gentle school,” says Ruth Drury, 17, who will enter her final year, or “college two”, in September. “It teaches you to accept people for who they are; that there are two sides to every story; to accept that you might be wrong. It teaches you fairness. It has definitely brought out the best in me.”

As in other Quaker schools, environmental issues are taken seriously, and pupils are encouraged to recycle and think about the sources of their clothes, food and other goods; to understand connections between one country’s riches and another’s poverty. Amnesty International is well supported, and in the build-up to the war in Iraq, parents and pupils were given the school’s blessing to join anti-war protests - with a busload travelling down to London.

Although less than 10 per cent of families who choose the school are Quakers, and although few staff are Quakers - Mr Small is an Anglican and the first non-Quaker head - the ethos is strongly upheld. The school is “doing a necessary job in a world where values have gone skew-whiff,” says Mr Small. He hopes Bootham offers values without dogma, based on the central Quaker premise that “there is that of God” in everybody and that all are equal in their spiritual search.

Pupils of all faiths are welcome: Mr Small says Bootham is marked by the same openness, trust and concern to treat all with the same degree of care as the Religious Society of Friends itself. “The Quaker approach takes nerve. In today’s climate it takes nerve to trust, but children at Bootham are relied on to tell the truth and, because of that, most of them do. You don’t penalise the majority of students for the very few who let the others down.”

In the closing stages of his headship, Mr Small has become increasingly troubled by the widening chasm between the underlying trust underpinning his own establishment and the lack of that quality in the national education system. The Government, he says, has backed itself into a corner and its ministers cannot admit they are wrong in tying pupils and teachers to a detestable and “increasingly examination-driven system that is so deadening”.

To demonstrate his point, he has often quoted from WH Auden’s “The Unknown Citizen”, whose life is measured by its outward conformity rather than inner happiness. The Government, he says, is measuring conformity when education should be about bringing out the individual worth of every child.

“It’s about recognising the light in every child from whichever direction it may come.” League tables are the death knell of this approach. “They are so misleading. So many factors have to be taken into account; what is being measured?”

Bootham, in fact, achieves highly. Most pupils take as many as 11 GCSEs to ensure “breadth” in the curriculum and, in the most recent lot of government rankings, it came within the top 20 in England for A-level results, and second only to Westminster among co-educational boarding schools. But Mr Small attaches a health warning to such results. “The figures are accurate but I don’t believe in them because I don’t know what they mean.” Of far greater importance is that “when youngsters leave here they leave with a sense of service and a willingness to think about things”.

Bootham is one of nine Quaker schools established by the Society of Friends in England and Wales since the end of the 18th century. The first, Ackworth, near Pontefract in West Yorkshire, was founded by a doctor, John Fothergill, with an emphasis on quiet reflection and service. It was co-educational from the start. Bootham was founded for boys in 1823 by William Tuke, who had already established pioneering care for the mentally ill by setting up the Retreat in York. His wife, Esther, set up a school for girls - precursor to The Mount, the Quaker girls’ boarding school in York.

Quaker businesses have thrived in York, notably Rowntree, and the Rowntree family has influenced the school’s development. From the outset, Bootham has nurtured academic enquiry, particularly in science and mathematics - its pioneering natural history society is still running and still popular - confident that such enquiry would not hamper religious faith. Ahead of its time, it favoured simple regulation without corporal punishment.

Attending any of the schools does not come cheap. Quakers are sometimes tortured to think that parents pay up to pound;17,000 a year for the privilege, but comfort themselves with the belief that their schools act as important witnesses to Quaker values. Bootham tends to attract double-income professionals - doctors, lawyers, academics, educationists and a large number buying into independent education for the first time.

The school’s frontage is gracious and Georgian, a stone’s throw from the Minster, just outside the city wall. Its assortment of extensions, buildings and playing fields, squeezed between the narrow streets of York, mark its expansion through the centuries. Jonathan Taylor, currently deputy head of Bedales, the progressive and liberal independent school in Hampshire, will take over headship in September of a school bursting at the seams, though, like all Quaker schools, it is still comparatively small, with around 430 pupils.

When Ian Small became head, there were slightly more than 300 pupils, and he believes Bootham has reached capacity. Quakers value smaller schools, to give each pupil individual space to develop in his or her own way. There are sanctions within the school: pupils who transgress write out columns of words - a punishment introduced in the mid-19th century - and can be gated, confined to school premises. But most problems are sorted “on an individual basis”.

Mr Small leaves his headship to take up a research degree in 18th-century regional theatre at York University. A committed performer, he starred during his closing weeks at Bootham as Pooh-Bah, the Lord High Everything Else in York Opera’s production of The Mikado. But you couldn’t get a head less like The Mikado’s hysterical autocrat. As befits the school’s ethos, he’s been hands-on, directing drama productions, teaching AS-level theatre studies, running the first-year PSHE programme with the school nurse and serving teas and coffees at functions.

His role is just one aspect of the flat structure of the school. There is no prefect system, just a head girl and boy and two deputies (known curiously as “reeves”) chosen, not by the head or a school vote but by a committee of staff and pupils meeting over several weeks. “It’s not a popularity contest,” he says. “We do things more slowly here.”

Quakers don’t vote in meetings. Decisions are reached in unity “rather than unanimity” and doubts carefully minuted. Neither is there an annual prize-giving ceremony, on the basis that children should be encouraged to achieve their potential but not paraded.

The school’s development director, Jane Peake, was formerly a businesswoman. “When I was in business,” she says, “people were talking about moving to flatter structures, about teamwork, about respecting the ideas of everyone, including the man on the shop floor. That is what we have here. Pupils here expect staff and their peers to listen to them and not jump to conclusions. In return they give co-operation. The time has come for a school like this.”