John Hutton Balfour FRSE FRS FRCSE FLS MWS (15 September 1808 – 11 February 1884) was a Scottish botanist.

His original intention had been to seek ordination in the Church of Scotland but instead he started medical practice in Edinburgh in 1834 after studying abroad.

These appointments followed a protracted political struggle in which Balfour triumphed over his distinguished opponent, Joseph Dalton Hooker, a close associate of Charles Darwin.

In January 1862, he corresponded with Charles Darwin on botanical matters, recollecting their evenings together at the Plinian Society with his brother-in-law William A.F.

He also corresponded with the extraordinary and irascible botanist Hewett Cottrell Watson, an early phrenologist, evolutionist and advocate of the differential development of the human cerebral hemispheres.

Under Balfour's care the Royal Botanic Garden was enlarged and improved and a palm-house, arboretum, and teaching accommodation were built.

His son, Sir Isaac Bayley Balfour (1853–1922), became a distinguished botanist in his own right, serving as Sherardian Professor of Botany at Oxford University from 1884 to 1888, before returning to his father's old Chair at Edinburgh.

From 1877 he lived in Inverleith House within the then newly extended Royal Botanic Gardens, Edinburgh in his role there as Regius Keeper.