Aiton was born near Hamilton. Having been regularly trained to the profession of a gardener, he travelled to London in 1754, and became assistant to Philip Miller, then superintendent of the Chelsea Physic Garden. In 1759 he was appointed director of the newly established botanical garden at Kew, where he remained until his death. He effected many improvements at the gardens, and in 1789 he published Hortus Kewensis, a catalogue of the plants cultivated there. He is buried at nearby St. Anne's Church, Kew.
A second and enlarged edition of the Hortus was brought out in 1810–1813 by his eldest son, William Townsend Aiton.