Flett was awarded the Neill Prize (1898-1901) of the Royal Society of Edinburgh and was elected a Fellow of the Royal Society of Edinburgh in 1900, upon the proposal of James Geikie, Ben Peach, John Horne and Ramsay Traquair.
Flett served as President of the Edinburgh Geological Society, President of the Mineralogical Society, and President of the geology section of the British Association (1921) [REF].