The earliest reference to the Clan Macnaghten is in connection with great Pictish rulers of Moray. The name 'Nechten' which means "pure" or "clear" was popular in the Pictish royal line. The originator of the clan is believed to have been "Nechtan Mor" who lived in the 10th Century.

13th century Castle in Loch Awe

By the time of the Renaissance, Clan Macnaghten had developed four distinct branches, or "septs," each recognized by the Crown with its own coat of arms. The senior line, MacNauchtan of Argyll, is assumed to descend from Sir Gilchrist MacNauchtan, who was granted land in Argyll in the early 13th century by Alexander III, King of Scotland. Parchments from 1247 and 1267 bearing the seal of Sir Gilchrist MacNauchtan are among the oldest existing charters in Scotland. They took up residence on an island in Loch Awe called Fraoch Eilean, which name they used as a battle cry.

14th century and Robert the Bruce

During the 14th Century the MacNaghtens were opposed to Robert the Bruce and his claim to the throne of Scotland; however, he did eventually become King Robert I of Scotland. As a result, the MacNaghtens forfeited many of their lands. Clan Macnaghten also fought against Robert the Bruce at the Battle of Dalrigh in 1306. The fortunes of the clan were restored, however, when King David II of Scotland granted them lands in Lewis.