The Farquharson clan history started with Finla Mor, the royal standard bearer slain at the Battle of Pinkie in 1547, though they trace there lands and ancestry back to Farquhar, 4th son of Alexander Cier of Rothiemurcus.

The clan's lands were in the Braes of Mar, Aberdeenshire, and they joined the Clan Chattan in 1595 to come under their protection from some of the more aggressive neighbouring clans. Braemar castle was built by the Erskines to reduce the influence of Farquharsons in the area as they tried to re-establish themselves as the Earls of Mar. Braemar Castle ended up in the hands of the Farquharsons as they earned themselves a reputation as the 'Fighting Farquharsons'.

The Farquharsons were devout followers of the Stuarts fighting for Charles I as royalists and supporting Charles II. They fought under the Clan Chattan for the Jacobite cause in both the 1715 and 1745. They also fought at Culloden led by Francis Farquharson, who was captured and imprisoned in the Tower of London.