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son of James Paton, a stocking manufacturer in a small way, was born in the parish of Kirkmahoe near Dumfries, Scotland, on 24 May 1824. He went to the parish school at Torthorwald, then helped his father at his trade, and having earned a little money, went to Dumfries Academy for a short period. He worked for the Ordnance Survey of Scotland and as a harvester, and then applied for a position at Glasgow at £50 a year as a district visitor and tract distributor. There were two candidates and it was decided that they should share the wages and the work, and study at the Free Normal Seminary. Paton later taught at a school for a season before being appointed an agent in the Glasgow City Mission. He worked at Glasgow for 10 years among the poorest and most degraded people in the city with much success, and carried on his studies at the same time at the university of Glasgow, and the Reformed Presbyterian Divinity Hall. In December 1857 he was licensed as a preacher, in March 1858 was ordained, and in April he set sail to the New Hebrides as a missionary. On 30 August he arrived at the harbour at Aneityum. He established himself on the island of Tanna, the natives of which were savage cannibals who had previously killed or driven away other missionaries. He had married before leaving Scotland, Mary Ann Robson, and in February 1859, about three months after landing, she and her infant son both died. Paton though ill and depressed stayed on, as he feared if he once left the island he might not be allowed to land again. He was in constant danger of death, at one meeting of the warriors it was proposed that Paton and his associates should be killed, and they were only saved by the advocacy of one of the chiefs. He had recurring attacks of fever and ague, the natives blamed him for every misfortune which befell them, and the bad behaviour of white traders, often engaged in the kanaka traffic, increased his difficulties. He risked his life frequently in endeavouring to persuade the natives to give up their tribal wars. Eventually the mission station was attacked, and Paton, after spending a night in a tree surrounded by savages seeking his life, just succeeded in making his way to another part of the island, where he was found by a vessel sent to rescue him.

Paton had made up his mind that the mission must have a ship of its own. He went to Sydney, toured Australia and raised £5000 for the mission, and in May 1863 sailed for London. In Scotland he was appointed moderator of the supreme court of the Reformed Presbyterian Church, and made a successful tour of the country on behalf of the missions. In 1864 he married Margaret Whitecross, and in January 1865 arrived in Australia again. He found that the mission ship for which he had worked so hard had been able to do useful work, but there was a considerable debt for the crew's wages. Paton promptly obtained subscriptions sufficient to pay the debt. Thereafter the Sunday Schools of Australia provided for the upkeep of the vessel. In 1866 Paton was transferred from his church in Scotland to the Presbyterian Churches of Australia, and in August of that year was sent to Aniwa, an island less savage than Tanna. There he steadily made way, though the first church built was blown down during a hurricane, and the mission ship was wrecked in 1873. Paton went to Australia and New Zealand and raised the money for a new ship. As time went on it was found necessary to have a vessel with steam power, and Paton travelled to Great Britain where he frequently addressed nine meetings in a week and carried on an immense correspondence. In 18 months he collected £9000, of which £6000 was spent on the new ship, and the other £3000 formed into a fund for the training of missionaries. In 1889 he published his autobiography, John G. Paton Missionary to the New Hebrides, written at the request and with the help of his younger brother, the Rev. James Paton. It had an immediate success and ran into several editions. Paton was spending much of his time from 1886 to 1892 between the islands and Australia, and found the trading in intoxicants and firearms was causing immense harm to native populations. He felt that Great Britain, France and the United States, should make a joint effort to stop it. In 1892 he was sent to the Pan-Presbyterian council which assembled at Toronto. Going on to New York and Washington he endeavoured to have an agreement made between the three powers, but the negotiations fell through. He then went to Great Britain where he was everywhere received with enthusiasm. He returned to Australia towards the end of 1894 and handed to the moderator of the Presbyterian Church of Victoria the sum of £13,527, of which £1000 represented part of the profits from his autobiography. In 1900 he again visited the old world with equally successful results. His eightieth birthday was celebrated at Melbourne on 24 May 1904 by a great meeting at the Scots church. He made his last visit to Aniwa in June 1904, and on 16 May 1905 his devoted wife died. She was the author of Anecdotes on the Shorter Catechism, Letters and Sketches from the New Hebrides, and Helen Lyall, a Biographical Sketch. Always hoping that he might be able to visit the islands again, Paton died at Canterbury, a suburb of Melbourne, on 28 January 1907. He was survived by five sons and one daughter. One of his sons, the Rev. Frank H. L. Paton, also a missionary to the New Hebrides, was the author of Lomai of Lenakel, Patteson of Melanesia, and with A. K. Langridge, John G. Paton, Later Years and Farewell.

Paton was a great missionary, fearless, sincere, seeking nothing for himself, completely wrapped up in his work. He was a marvellous collector for missions, often working to the limit of his endurance, and only anxious that none of the money collected should be wasted in unnecessary expenses.