James Duncan was born on 1 February 1813 at Airdrie, near Glasgow, Scotland, the son of a Lanarkshire baker, James Duncan, and his wife, Marrian Hill. After studying at Glasgow University from 1836 to 1838, he attended the Theological Hall of the Reformed Presbyterian Church at Paisley from 1839 to 1841, and was ordained on 22 September 1842 as the church's first missionary to the Maori. On 20 September 1842, at Carriden, West Lothian, he married Christian Struthers; they were to have four children.
Arriving at Wellington on the Phoebe in April 1843, Duncan began travelling among the local tribes, and conducted services at the Scotch Church (later called St Andrew's). He began his mission in Manawatu in June 1844. At Te Maire his overtures were welcomed by a branch of Ngati Raukawa led by Taikapurua and his relative Ihakara Tukumaru, who offered him a mission site at Kapahaka. The district already had an association with the Anglican mission and Octavius Hadfield objected to Duncan's intrusion, to the consternation of the local Maori, who had no understanding of interdenominational rivalries. They decided, however, that a resident missionary was preferable to one at a distance.
In late 1844 Duncan's house at Kapahaka burned down. The population there had declined and he decided to move to Te Maire, which he judged more suited to 'stationary labours'. There he was joined in January 1845 by the Reverend John Inglis. During August and September 1845 his missionary activities were curtailed by ill health, and he spent October in Wellington, where he preached to the Scottish settlers and received medical treatment. After his return in November, the ship carrying some of his goods was wrecked at the mouth of the Manawatu River, destroying his provisions and damaging his library.
The subsequent progress of the mission proved disappointing. Few attended its school or its religious services. It was also involved in running battles with the nearby Anglican mission. Duncan and Inglis were reduced to giving their 'parishioners' some training in farming and commercial practice and to growing wheat for sale.
Duncan left Manawatu for Wellington about November 1846, on medical advice. Inglis carried on alone until May 1847, when the government advised settlers to leave the district in the wake of the Gilfillan murders of April 1847. In March 1848 Duncan returned and re-established the mission at Te Awahou (Foxton). A series of epidemics, renewed migration and the sustained opposition of Hadfield made his position untenable. Various of his Ngati Raukawa supporters threatened to withdraw to Rangitikei in pursuit of old land claims, while the more promising went back to Hadfield, leaving only four behind. The growing materialism and the widespread 'apathy and indifference' of the people to religion completed his disillusionment. Duncan now devoted himself chiefly to the spiritual needs of the growing numbers of European settlers along the banks of the Manawatu River.
His final break with the mission was precipitated by a further quarrel with Hadfield in 1860. Duncan denounced a Te Ati Awa petition calling for the removal of Governor Thomas Gore Browne over the Waitara affair as a forgery, inspired, if not composed, by Hadfield. He in turn was accused of being in government pay and of having received large grants of land, a charge he was easily able to rebut.
Duncan had by now settled down at Te Awahou, where he built a church on his own land, although he preached throughout the district. In 1861 he was appointed by the Presbytery of Wellington to labour in the Rangitikei–Manawatu district. As convener of the Maori and Foreign Missions Committee of the Presbyterian Church, he persuaded that body to send a missionary to the New Hebrides. In 1861 he was involved in negotiations for the union of the various Presbyterian churches in New Zealand. He served as moderator of the General Assembly of the northern Presbyterian Church of New Zealand in 1863. In 1872 he gave up his Maori work in the lower Rangitikei to Abraham Honoré, in favour of his parish at Te Awahou and the needs of a new bush settlement at Palmerston North. In 1884 he was elected moderator of a recently established presbytery at Wanganui, and in 1888 he was again moderator of the General Assembly. He eventually retired in 1897, but was on hand in 1901 to second the motion for union between the northern Presbyterian Church and the Synod of Otago and Southland. He died at Foxton on 30 December 1907.