The origin of the name Fergusson or Ferguson, "son of Fergus" (MacFhearguis in Gaelic), is shrouded by the mists of time. Medieval historians recorded a tradition that the founder of Scotland's monarchy was a Fergus who lived in Ireland about 300 B.C. Historical research dating from the 13th century confirms that by 500 A.D. the Scots under King Fergus Mor had left Northern Ireland and became established in Dalriada, now Argyll. From Fergus Mor, with a few early exceptions, descend all subsequent kings and queens of the Scots, including the present Queen of Great Britain. St. Columba of Iona (6th century A.D.) was a scion of Fergus Mor's royal line.

In one of the oldest documents of ancient Scottish history, the "Tract on the Men of Albyn", Fergusson is the only modern clan name mentioned. Some writers believe the Fergussons had their day as a powerful clan prior to the 13th century and became dispersed from Argyll (Dalriada) as the Scots spread into other parts of Scotland. Before the 18th century, at least five groups of Fergussons possessed lands and lived in the style of a clan under their respective chiefs in Argyll, Perthshire, Aberdeenshire, Dumfriesshire, and Ayrshire. Today, the Kilkerran Fergussons in Ayreshire and the family of Fergusson of Baledmund and the Fergussons of Balquhidder, both in Perthshire, are still owners of extensive lands.