The eldest son of Edward Clarke and Anne Grenfield, and brother of Edward Daniel Clarke, he was born on 17 December 1766 at Mahon, Minorca where his father was at the time chaplain to the governor. He was educated at Uckfield School and then at Tonbridge School under Vicesimus Knox. Matriculating at St John's College, Cambridge in 1784, he did not complete a first degree.
Having taken holy orders, Clarke was in 1790 appointed to the rectory of Preston, Sussex. About the beginning of 1791 he was living in Sussex with his mother, taking in the refugee Anthony Charles Cazenove for half a year. In 1792 he was living at Eartham with William Hayley; Thomas Alphonso Hayley made a bust of him.
Clarke in February 1795 entered the Royal Navy as a chaplain; and served, 1796-9, on board HMS Impetueux in the Channel fleet, under the command of captain John Willett Payne, by whom he was introduced to George, Prince of Wales. It was the end of his service afloat, after George appointed him his domestic chaplain and librarian.
In 1806, Clarke took the degree of Bachelor of Laws (LLB) at Cambridge, and in 1816 the further degree of Legum Doctor (LLD) was conferred on him per literas regias. George had him made historiographer to the king on the death of Louis Dutens in 1812. He was also a Fellow of the Royal Society.
From 1815 for a short period Clarke was in contact with Jane Austen about her novel-writing: they were introduced by Austen's friend the surgeon Charles Thomas Haden. Having shown Austen round the library at Carlton House in November, and arranged that George should have Emma dedicated to him, Clarke also made suggestions in correspondence for Austen's future writing. These she mocked in the satirical manuscript Plan of a Novel, according to Hints from Various Quarters, not published in her lifetime.
Clarke was installed canon of Windsor, 19 May 1821; and was Deputy Clerk of the Closet to the king. The canonry came about by compromise between George IV (as George had become) and Robert Jenkinson, 2nd Earl of Liverpool the Prime Minister, in a clash over preferment for Charles Sumner. Under a deal struck, Sumner took on Clarke's royal appointments.
Clarke died on 4 October 1834.
In 1798, Clarke published a volume of Sermons preached in the Western Squadron during its services off Brest, on board HM ship Impetueux (1798; 2nd edit. 1801). With John McArthur, a purser in the navy and secretary to Samuel Hood, 1st Viscount Hood at Toulon, he started the Naval Chronicle, a monthly magazine of naval history and biography, which ran for twenty years. In 1803 he published the first volume of The Progress of Maritime Discovery, which was not continued. He issued in 1805 Naufragia, or Historical Memoirs of Shipwrecks (3 vols.). Its subtitle "of the Providential Deliverance of Vessels" reflects its traditional content, harking back to James Janeway.
In 1809, with McArthur, Clarke published his major work, the Life of Lord Nelson (2 vols.; 2nd edit. 1840). It mixed official and private letters, and made questionable use of its sources. Robert Southey criticised it destructively in the Quarterly Review, a culmination of his literary feud with Clarke that led also to Southey writing his own Nelson biography.
In 1816, Clarke published a Life of King James II, from the Stuart MSS. in Carlton House (2 vols.). The work contains portions of the king's autobiography, the original of which is now lost; in the Dictionary of National Biography it was considered to be the work of Lewis Innes, where Clarke attributed it to his brother Thomas Innes. A modern scholarly view is that the work was written in two parts by different Jacobite courtiers, the first part (to 1677) being by John Caryll, the second by William Dicconson. David Nairne assisted Caryll.
- Morriss, Roger. "Clarke, James Stanier". Oxford Dictionary of National Biography (online ed.). Oxford University Press. doi:10.1093/ref:odnb/5504. (Subscription or UK public library membership required.)
- "A Field Guide to the English Clergy' Butler-Gallie, F p149: London, Oneworld Publications, 2018 ISBN 9781786074416
- Mark Antony Lower, The Worthies of Sussex (1865), p. 63: "In fact, Uckfield school enjoyed considerable celebrity. During the mastership of the Robert Gerison, James Stanier Clarke, and his brother Edward Daniel Clarke, the well-known traveller, received their rudimentary education there..."
- Stephen, Leslie, ed. (1887). . Dictionary of National Biography. 10. London: Smith, Elder & Co.
- "Clarke, James Stanier (CLRK784JS)". A Cambridge Alumni Database. University of Cambridge.
- John Askling, Autobiographical Sketch of Anthony-Charles Cazenove: Political Refugee, Merchant, and Banker, 1775–1852, The Virginia Magazine of History and Biography Vol. 78, No. 3 (Jul. 1970), pp. 295–307, at p. 296. Published by: Virginia Historical Society. Stable URL: https://www.jstor.org/stable/4247580
- Lewis Leary, Joel Barlow and William Hayley: A Correspondence, American Literature Vol. 21, No. 3 (Nov. 1949), pp. 325–334, at p. 330. Published by: Duke University Press. Stable URL: https://www.jstor.org/stable/2921248
- Stephen, Leslie; Lee, Sidney, eds. (1891). . Dictionary of National Biography. 25. London: Smith, Elder & Co.
- Lynda Pratt (1 November 2007). Robert Southey and the Contexts of English Romanticism. Ashgate Publishing, Ltd. p. 104. ISBN 978-0-7546-8184-7. Retrieved 4 September 2013.
- John Halperin, Jane Austen's Lovers, SEL: Studies in English Literature 1500–1900 Vol. 25, No. 4, Nineteenth Century (Autumn, 1985), pp. 719–736, at p. 734. Published by: Rice University. Stable URL: https://www.jstor.org/stable/450671
- Paul Poplawski (1 January 1998). A Jane Austen Encyclopedia. Greenwood Publishing Group. pp. 238–9. ISBN 978-0-313-30017-2. Retrieved 4 September 2013.
- Lee, Sidney, ed. (1898). . Dictionary of National Biography. 55. London: Smith, Elder & Co.
- J. C. D. Clark, Providence, Predestination and Progress: Or, Did the Enlightenment Fail?, Albion: A Quarterly Journal Concerned with British Studies Vol. 35, No. 4 (Winter, 2003), pp. 559–589, at pp. 564–565. Published by: The North American Conference on British Studies. Stable URL: https://www.jstor.org/stable/4054295
- William Arthur Speck (2006). Robert Southey: Entire Man of Letters. Yale University Press. p. 137. ISBN 978-0-300-11681-6. Retrieved 4 September 2013.
- Lee, Sidney, ed. (1892). . Dictionary of National Biography. 29. London: Smith, Elder & Co.
- Edward Gregg, New Light on the Authorship of the Life of James II, The English Historical Review Vol. 108, No. 429 (Oct. 1993), pp. 947–965, at p. 961. Published by: Oxford University Press. Stable URL: https://www.jstor.org/stable/575537
- Corp, Edward. "Nairne, David". Oxford Dictionary of National Biography (online ed.). Oxford University Press. doi:10.1093/ref:odnb/46463. (Subscription or UK public library membership required.)