The Original Botanic Garden was founded by the University of St. Andrews in 1889 in the precincts of St. Mary's College by a group of enthusiasts led by Dr John Wilson. The original garden was about 0.1ha (0.25 acres) in size and consisted of 78 regularly-shaped beds laid out according to the Bentham and Hooker plant classification. By 1960 the old Botanic Garden covered 2.8ha (7.8 acres). In addition, plants were grown in a variety of soil and climatic conditions in other parts of the University.

The Present Botanic Garden of 7.5ha (18.5 acres) was created from two fields in the early 1960s to cater for expansion of the collection and release the town centre lands for other purposes. In 1987, the Garden was leased to the Local Authority, then NE Fife District Council, now Fife Council which has been responsible for management ever since. The Hon. Curator is Bob Mitchell (formerly Curator) who, together with Jim Mackie, the recently retired Head Gardener, has designed and developed the Garden since 1962.