He was educated at Galashiels, chiefly by the Reverend Robert Balmer, until in 1806, at age thirteen, he went to the University of Edinburgh, from which he graduated Doctor of Medicine in 1814.
He held the Chair for the shortest period of any holder to date, resigning from his position immediately after giving his opening address. After his graduation he was appointed Physician"s Clerk to James Hamilton, Professor of Midwifery at the University of Edinburgh, a position he relinquished in 1817. In 1824 Lee accepted an appointment as personal physician to Prince Mikhail Semyonovich Vorontsov, Governor-General of the Crimea.
Through this office he met Alexander I of Russia in 1825.
He described his experiences in Russia in the book The Last Days of Alexander and the First Days of Nicholas, published in 1854. Returning to London in 1827, Lee was appointed in 1830 a Fellow of the Royal Society, an institution with which he maintained a long and acrimonious relationship, particularly over the disputed award of a Royal Medal to Thomas Snow Beck.
Through the offices of William Lamb, 2nd Viscount Melbourne, Lee was appointed Regius Professor of Midwifery at the University of Glasgow in 1834. However, he resigned after his opening speech and returned immediately to London.
Between 1835 and 1866 he was lecturer at Street George"s Hospital, London, on midwifery and the diseases of women.
In 1841 he was elected a Fellow of the Royal College of Physicians. He delivered their Lumleian lectures in 1856, their Croonian Lecture in 1862 and their Harveian oration in 1864, the last time it was delivered in Latin. Lee died in London in 1877.
He is buried at Kensal Green Cemetery, London.