John Thornton was born at Kentish Town, London, England, on 19 March 1844, the son of John Thornton, a coachman, and his wife, Mary Ann Bott. John was educated privately and at Highbury College, London, where he gained a first-class certificate. In 1864 he left England for India to engage in educational work with the Church Missionary Society in the state of Andhra Pradesh. On 18 October 1865, at Bangalore in southern India, he married Emily Scudder Smith.
Thornton qualified himself to take charge of a vernacular training school at Machilipatnam, educating Christian trainees for teaching in rural schools, and subsequently spent two years reorganising a high school at Elūru. In 1875 the Thorntons were forced to leave India for health reasons, and John accepted the rectorship of Oamaru Grammar School, in Otago, New Zealand. In 1878, after only two years in Oamaru, he was appointed headmaster of Te Aute College, the Anglican boarding school for Maori boys in Hawke's Bay.
At this time Te Aute College was little more than a primary school like the other Maori denominational boarding colleges. But from the beginning Thornton insisted on developing its curriculum along the lines of an English grammar school, with a solid academic bias. In this aim he was actively supported by Samuel Williams, the school's founder and provider. Thornton later wrote, 'I tried from the very first to raise the standard of the school, and…conceived the idea of preparing Maori boys for the matriculation examination of the New Zealand University.…I saw that the time would come when the Maoris would wish to have their own doctors, their own lawyers, and their own clergymen, and I felt it was only just to the race to provide facilities for their doing so'. The success of this philosophy was soon demonstrated. By 1883 James Pope, the organising inspector of native schools, was describing the standards being reached at Te Aute in mathematics and science as equal to those of any secondary school in the country.
By 1900 the high academic standards developed under Thornton's leadership had made Te Aute pre-eminent among the Maori denominational boarding colleges, with several boys each year passing the matriculation examination and entering university. Thornton was also innovative in appointing old boys as masters: during the early years the two junior classes at the college were taught by Walter Wi Paipa, and later Reweti Kohere and Tutere Wi Repa were assistant masters. Like most of his European contemporaries Thornton held an assimilationist view of the interaction between Maori and European culture, believing that the Maori race must emulate the European in order to survive. However, he worked persistently with Samuel Williams in the late 1890s to persuade the University of New Zealand to establish a chair in Maori, or at least include Maori as a subject for the BA degree, and he encouraged students to speak Maori for fear that the language might die out.
In 1906 Thornton's achievements came under challenge when the Royal Commission on the Te Aute and Wanganui School Trusts was established to consider, among other questions, whether there was sufficient provision for manual and technical instruction at Te Aute. George Hogben, the inspector general of schools, along with others who appeared before the commission, recommended that the college 'drop Latin, Euclid, and algebra out of the…curriculum altogether' and increase agricultural and manual instruction. The most academically able students could be sent to ordinary secondary schools. Hogben predicted that eventually Te Aute would have no role to play in preparing boys for matriculation and higher education.
Thornton vigorously defended the existing academic curriculum. He argued that Maori opinion favoured academic instruction, the attitude of Maori parents being, 'We do not send our boys to Te Aute to learn to plough – we can teach them at home'. 'To them', Thornton continued, 'Te Aute is what Wanganui and Christ's College are to the Europeans'; if boys were not taught trades at those institutions, why should they be at Te Aute? He also told the commission that Maori boys needed to be kept together because they required a particular style of teaching; it was necessary to know the Maori mind, and the kind of special attention needed was unlikely to be available at other institutions. Maori agriculture, he believed, would be better promoted by a separate Maori institution along the lines of Canterbury Agricultural College at Lincoln.
Thornton's defence of the existing academic emphasis at Te Aute proved to be only partially successful. The commission recommended that greater prominence be given to manual and technical instruction in agriculture, and the Department of Education pressured the school's trustees accordingly. The resultant policies eventually restricted the opportunities for further academic work that Thornton had established.
Thornton's chief significance as an educator was, first, his belief that Maori boys were as capable as their European peers of entering the full range of available occupations, including the professions; and second, his establishment of a curriculum which enabled this philosophy to become a reality. This was a particularly significant achievement in the context of the prevailing official view that Maori education should be practical, designed to encourage Maori to stay in the rural areas and not compete with Europeans for occupations in the towns. His belief soon became a self-fulfilling prophecy. It was no coincidence that during his tenure at Te Aute a group of extraordinarily able Maori students had their talents identified and encouraged. They included Apirana Ngata, Reweti Kohere and Tutere Wi Repa of Ngati Porou; Te Rangi Hiroa (Peter Buck) of Taranaki; Maui Pomare of Te Ati Awa; and Edward Ellison of Ngai Tahu, all of whom became prominent politically and in their professions. These students formed the nucleus of the Te Aute College Students' Association, also called the Young Maori Party, which was established by graduates of Te Aute in 1897. Its aims were to promote better health and educational opportunities for Maori people. Thornton encouraged the association and acted at various times as its secretary, president and chairman.
In addition to his educational achievements, John Thornton was active in Anglican church affairs as a lay member of the Waiapu cathedral chapter and the diocesan synod. He published The story of India in 1912. That year he retired as headmaster of Te Aute College due to ill health, and died at Kohanga, Havelock North, on 4 July 1913. Emily Thornton had died 14 years earlier, on 14 May 1899. They were survived by two sons and one daughter.