He began college at the age of 16 at Mundell's School on the West Bow close to his family home, and then studied medicine under William Cullen and Joseph Black at the University of Edinburgh,[2] graduating with a doctorate (MD) in 1772.

On 12 April 1782 Rutherford was one of the founding members of the Harveian Society of Edinburgh and served as President in 1787.

[5] At this time he lived at Hyndford Close on the Royal Mile[6] a house he (or his father) had purchased from Dunbar Douglas, 4th Earl of Selkirk He was a professor of botany at the University of Edinburgh and the 5th Regius Keeper of the Royal Botanic Garden Edinburgh from 1786 to 1819.

[8] Around 1805 he moved from Hyndfords Close to a newly built townhouse at 20 Picardy Place at the top of Leith Walk, where he lived for the rest of his life.

[12][13] When Joseph Black was studying the properties of carbon dioxide, he found that a candle would not burn in it.