The most famous Highland branch of the Macraes were to be found in Kintail in Wester Ross where they settled in the 14th century. Prior to that they appear to have inhabited the lands of Clunes on the Lordship of Lovat in the Beauly district. The founder of the Kintail branch is said to be Fionnla Dubh MacGillechriosd who died in 1416. His descendants from 1520 became the keepers of Eilean Donan, the stronghold of the Mackenzies of Kintail. Like the Maclennans, the Macraes faithfully supported the Mackenzies and were referred to as the "Mackenzies shirt of mail".

Duncan, 5th of Kintail fatally wounded Duncan Gorm the chief of the Macdonalds of Sleat in 1539, protecting the castle. Some time later Duncan Macrae, Chamberlain of Eilean Donan was granted the estate of Inverinate that remained in the family for over 200 years. The Macraes as loyal followers of the Mackenzies were not only constables of Eilean Donan Castle but were also Chamberlains of Kintail and Vicars of Kintail as well as sharing with them their hatred of the Macleods. The Rev. Farquhar Macrae of Inverinate (1580-1662) combined his offices as Chamberlain with that of Vicar of Kintail for over forty years. His grandson, Duncan Macrae of Inverinate was the compiler of the famous Fernaig Manuscript 1688-93. However due to his marriage to one of the daughters of John Macleod of the island of Raasay, he was deprived of his inheritance.

Although the Clan Macrae was not out in the '45, many of the Macraes took part in the rising and in fact their reputation as warriors continued over the generations and earned them the title "the wild Macraes". Other cadet branches include the Macraes of Conchra who descend from one of the sons of the Rev. Farquhar Macrae, and the Macraes of Clunes who stood in high favour with the Frasers of Lovat. In 1909, Sir Colin Macrae of Inverinate claimed the chiefship of the clan but the claim was opposed by a descendant of Conchra and hence there is no chief of the Clan Macrae today.