The MacGillivrays were an important clan in the midwestern isles even before King Somerled, Lord of the Isles, drove the Norsemen out of the area in the middle of the twelfth century. When Alexander II subdued Argyll in 1222, the Clann Mhic Gillebrath were   dispersed. Some of the clan remained in Mull and Morvern. Tradition asserts that Gillivray, the progenitor of the clan, placed himself under the protection of the chiefs of the clan Macintosh. The clan thereafter belonged to the Clan Chattan Confederation

The Macgillivrays were first accurately recorded in Dunmaglas in 1549. At the great gathering of the Clan Chattan in 1609, when all bound themselves in loyalty to the young Mackintosh chief and in mutual support, the 'haill kin and race of Macgillivray' was represented by Malcolm of Dalcrombie and Duncan Macfarquhar of Dunmaglas. This is a classic example of the use of patronymics and the territorial designations common in the Highlands before the use of what would now be popularly considered surnames became widespread in the eighteenth century.

The MacGillivrays were supporters of an episcopacy in the church, and this caused them to be persecuted by their Calvinist and presbyterian neighbours. In common with most of the confederated Clan Chattan families, the MacGillivrays were staunch Jacobites, and they fought in both the Fifteenth and in the Forty-five. In 1745 the chief of the MacKintoshes was an officer in a Hanoverian regiment. His wife, a formidable lady with distinct Jacobite sympathies, summoned Alexander MacGillivray and placed him in command of the regiment raised by Clan Chattan. MacGillivray was at the head of his men at Culloden where he fell along with many of his followers, and the graveyard at Dunlichity commemorates the many Macgillivray fallen. After Culloden, many emigrated across the Atlantic where their spirit of independence and fortitude made many successful, particularly as traders.

William MacGillivray became head of the Canadian Northwest Company and member of the Legislative Council of Lower Canada. The MacGillivrays have become organised and active again in this century, and there are clan societies throughout the world.