They became foundation members of the church at Brougham Place at the constituting meeting on 20 October 1859. Jefferis formed the North Adelaide Young Men’s Society in 1860. He was the minister of the congregation throughout the period when the church building was being constructed: the first stage from 1860-61, when the foundation stone was laid and the shell of the building was erected; the second stage in 1864 when the interior was completed and the external staircase and galleries added, and the final stage from 1871 to 1872 when the tower was constructed. Mary Louisa died in 1864 after giving birth to their third child. He married Marian Turner in Melbourne in 1866. He was several times chairman of the Congregational Union and promoted Protestant Union and non sectarian education.
James Jefferis played an important role in the foundation of the University of Adelaide. William Watson Hughes, who had acquired a large fortune from mining copper, supported the proposal of a Union College to train ministerial students and offered an endowment of £20,000. James Lyall, Hughes’ pastor, suggested to Jefferis that the sum should go rather to the establishment of a university in Adelaide. James Jefferis enthusiastically took up the idea and Hughes was persuaded to redirect his donation for this purpose. The University Act was passed in 1874 after vigorous debate in both houses.
He was called to Pitt Street Congregational Church in Sydney in 1877. There he became a well known preacher and lecturer, and a favourite subject of the cartoonists of the Bulletin. He was a prominent advocate of federation of the Australian colonies into a single Commonwealth.
He left Sydney for England in 1889. He ministered at New College Chapel and Belgrave Church in Torquay. However, he felt like a stranger at home. In 1894, he accepted a call back to the Brougham Place Congregational Church and ministered there until his retirement in 1901. During this time, a referendum on federation was held. In 1898 the people of the six separate Australian colonies voted to establish a federated ‘Commonwealth of Australia’ whose centenary we celebrate this year. In the campaign preceding that vote, the South Australian Council of Churches petitioned its member churches actively promoting a ‘yes’ vote. The letter bearing that recommendation was drafted by a Congregational minister, Dr James Jefferis, of the Brougham Place church.
Jefferis received the criticism of the Advertiser for this stance which was, it claimed, "beyond the province of the pulpit". "If the pulpit had nothing to say at such a moment of national significance," Jefferis retorted, its ministers would be rightly denounced as "dumb dogs that cannot bark". It is perhaps no co-incidence that the referendum question received its strongest metropolitan support in the electorate of North Adelaide.
In all, he was the minister of this church for 25 years. He and Marian and their family remained members of this congregation until his death. James Jefferis died at his summer home in Victor Harbour on Christmas Day, 1917. A memorial window was unveiled to him on 19 October 1919, the sixtieth anniversary of the church. On it was inscribed the opening lines of the Confessions of St. Augustine: “Cor nostrum inquietum est donec requiescat in Te.” [Our hearts are restless until they rest in you] His wife, Marian, survived him and died in 1930.
Dr James Jefferis has received the title of "Prophet of Federation". Historian, Dr Walter Phillips, of the La Trobe University in Melbourne, wrote his biography which was published in 1993.
Excerpt from In Stow's Footsteps: a chronological history of the Congregational Churches in S.A. 1837-1977, by the late John Cameron (pub. 1987):
"It was the Rev. T.Q. Stow who invited the Rev. James Jefferis to come to S.A. to help form a church at North Adelaide. Jefferis began his ministry in Temperance Hall, North Adelaide in May 1859 and a fellowship was formed in October of that year.
The Brougham Place church was opened in February 1861 and could seat 800 persons. Jefferis filled the church. [He] preached a 'progressive theology' and, at a time when many saw religion and science as enemies, he encouraged his congregation to see science and philosophy also as witnesses to God's truth."