Fota Island, 316 ha in area and about 12km east of Cork City was originally owned by the Smith-Barry family, first records of which date from soon after the Norman Conquest when their ancestor Philip de Barri was granted lands in South Cork by Henry II. A manor was established at Barryscourt and the family seat became Barryscourt Castle, a 15th century fortified house 3km from Fota. The Smith-Barry family decided to enlarge the hunting lodge on Fota Island in the early 19th century and Sir Richard Morrison, one of Ireland's foremost architects, transformed it into a splendid example of Regency architecture containing some of the finest neo-classical interiors found in Ireland.

The favourable Gulf Stream-influenced climate, favouring the growth of tender plants, was recognised in the early 19th century and successive generations of the Smith-Barry family laid out and developed the gardens and introduced many exotic species from plant collectors working in Asia, Australasia, and North and South America. After the death of the last resident member of the family, Hon. Mrs Bell in 1975, the gardens were acquired by University College, Cork, who considerably extended the Arboretum. After fifteen years they sold the estate to a development company, but subsequently the Arboretum & Gardens, along with the House, were leased to Fota Trust. In 1996 the Arboretum & Gardens were transferred to state ownership and came under the care and management of Duchas - The Heritage Service. Duchas continued the policy of planting exotic trees and shrubs for many years until the property was transferred to the Office of Public Works (OPW).