The earliest record of Kinfauns dates from 1382 when Robert II gave the eastern half of the lands to James Stewart, his natural son. The western half was given to James's younger brother, Walter. On James's death the lands reverted to the Crown. In the early 15th century, the estate was acquired by Thomas de Charteris and remained in this family until 1616. In 1647 it had passed to Thomas Blair of nearby Balthayock. In 1671, the Blair heiress, Anna, married Alexander Carnegie who assumed the name of Blair when they acquired Kinfauns shortly after their marriage. Their granddaughter, Margaret, married the 11th Baron Gray in 1741. They had four sons and six daughters, one of whom, Jean, married the 9th Earl of Moray, and this link resulted in the Moray family acquiring Kinfauns approximately 150 years later.
Three of the four sons of the 11th Lord Gray held the title following his death in 1782. His youngest son, Francis, succeeded as 14th Lord Gray in 1807 and it was he who commissioned Robert Smirke to build the Castle near the site of the previous house. He was a popular and respected local figure who did as much to improve the neighbourhood as he did to improve his own direct environment. Statistical accounts show that the population of the village of Kinfauns increased by some 27% between 1791-1821 when his improvements were advancing. W.S. Gilpin, nephew and pupil of William Gilpin, the English clergyman and author who was a pioneer of the picturesque, is reputed to have been consulted, amongst others, as to the improvements but there is no available documentary evidence to confirm this. There are some unsigned landscape drawings of Kinfauns in the 1820s which have not been seen during the course of this study.
In 1842 Lord Gray died. His successor, the 15th Baron, was responsible for much of the Victorian conifer planting, some of which remains to the west of the house. The title passed to his sister, Madelina, who too died without issue two years later. The title of Baroness Gray passed then to Margaret, the granddaughter of the 12th Baron. She married the son of the 3rd Earl of Mansfield. When she died in 1878, the title of Lord Gray passed to a cousin, already the 14th Earl of Moray. Kinfauns was inherited by Edmund Archibald Stuart, nephew of the 10th Earl of Moray, who took the name of Gray. Edmund himself became the 15th Earl of Moray on the death of his kinsman in 1895. His brother, 16th Earl, inherited in 1901. In 1909 Kinfauns passed to another brother, Morton Gray Stuart, who succeeded as the 17th Earl of Moray.
The 17th Earl commissioned considerable improvements to the Castle and buildings on the Kinfauns estate, in the course of which, the architects F.W. Deas and R.S. Lorimer were employed. The 17th Earl is known to have been a keen gardener and encouraged the upkeep of the gardens at Kinfauns. He died in 1930. Thereafter the estates became the property of 'Scottish Estates Ltd' who sold off the land in lots. The Castle and part of the policies were purchased by Co-operative Holidays Association (now known as Countrywide Holidays Association), an organisation which promotes walking holidays all over Britain. Since then other parts of the policies have been sold off; Kinnoull Hill is now a public park. The Home Farm and other east cottages are private residences and further housing has been developed in and around the walled garden.