Educated at the Burgh School, Kirkwall, and George Watson’s College, Edinburgh, Flett entered the University of Edinburgh at the age of seventeen. His academic career, of which he left an account, was one of remarkable promise. He read first for the arts degree, and the classics left him with a lifelong love of Horace, Catullus, and Lucretius; the other subjects in the course were mathematics, physics, metaphysics, moral philosophy, English, and political economy. Having graduated a Master of Arts at nineteen, Flett proceeded to the Bachelor of Science in natural sciences and followed this with the medical degrees a Bachelor of Medicine and a Master of Surgery in 1894. He also received a Doctor of Science in 1900 and a Legum Doctor in 1912.
After practicing medicine for a short time, Flett returned to the University of Edinburgh to become assistant to the professor of geology, James Geikie, and subsequently was promoted to a lectureship in petrology. His earliest researches were on the stratigraphy and petrology of the rocks of his homeland. His five years as petrologist at Edinburgh gave Flett a sure grasp of the subject and a growing reputation, especially as a result of his studies of the monchiquitecamptonite suite of minor intrusions.
In 1910 Flett jointed the Geological Survey of Great Britain, succeeding Sir Jethro Teall as petrographer and quickly attaining district geologist status. In 1911 he returned to Edinburgh as assistant director in charge of the Geological Survey in Scotland. He became director of the Geological Survey of Great Britain in 1921, occupying this position with great distinction until his retirement in 1935.
Flett’s joint study with C. E. Tilley of the unusual cordierite-anthophyllite rocks of the aureole of the Land’s End granite is significant in metamorphic petrology, but he is remembered more generally for the formulation, with Henry Dewey, of the spilite suite, a worldwide type characteristic of early geosynclinal history. As Survey petrographer, Flett’s work ranged widely over the richly varied rocks of the British Isles and is recorded in contributions to thirty-six issues of the Survey’s Memoirs, covering areas as separated as Caithness and Meneage. Abroad, his best-known work arose from a Royal Society expedition to St. Vincent after the eruption of Soufrière in 1902; Tempest Anderson was his collaborator.
After 1911 Flett’s energies turned to administration, and it was his powerful leadership that left its mark on science. Some of the Geological Survey’s best work was done under him, such as the completion of the highly detailed mapping of the Tertiary volcanoes and the revision of the major coalfields. More than this, it was Flett’s determination that brought to fruition the move of the Museum of Practical Geology (now called the Geological Museum) from its Victorian site behind Piccadilly to the present splendid building in South Kensington.
Flett served as President of the Edinburgh Geological Society, President of the Mineralogical Society, and President of the geology section of the British Association.
Flett became increasingly deaf, but there were those who believed that his success as an administrator was due to his hearing only those proposals according with his own wishes.
John married Mary Jane Meason in 1897, and together they had four children.