The earliest reliable owners of Cairnburgh were the MacDougalls, who held the castle between at least 1249 and 1269. They were one of the three great branches of Somerled's descendants, the Lordship of the Isles in its earliest form, and their holdings spanned Lorn from the mainland out to Mull. When the Wars of Scottish Independence forced a choice between John de Balliol and Robert de Brus, the MacDougalls backed Balliol. Robert the Bruce eventually won the throne, and the Crown seized MacDougall lands including Cairnburgh. The castle passed briefly to the rising Clan MacDonald and then, in murky circumstances, to Clan MacLean, who held it through the most violent centuries of its career. By the early sixteenth century the MacLeans of Mull and their cadet branches controlled most of the surrounding waters, and Cairnburgh was their offshore stronghold, garrison and refuge.

In 1504 James IV came west to suppress a Hebridean rebellion. Domhnall Dubh, claimant chief of Clan Donald and last hope of the old Lordship of the Isles, had risen against Edinburgh, and the MacLeans had backed him. James responded by laying siege to Cairnburgh, the kind of campaign that exposed both the strength and the weakness of the castle's twin-island design. The defenders could resist a head-on naval assault. They could not endure a long blockade. The siege ended the rebellion in the west, though Domhnall Dubh would resurface decades later. The castle returned to clan control. Through the rest of the sixteenth century it stayed in MacLean hands, surviving as one of those Hebridean strongholds that mattered more than its modest size suggested simply because it sat on the right channels, watched the right waters, and could be reached only by people who knew the tides.

The seventeenth century was rougher. In 1647, during the War of the Three Kingdoms, the Covenanter general David Leslie took the castle briefly. A decade later Oliver Cromwell's New Model Army came up the coast and torched what remained. The MacLeans rebuilt. In 1679 the Campbells came, an old feud now expressed through court orders and warrants of ejection, and Cairnburgh held them off. In 1692, the year Glencoe taught the Highlands a different lesson, the Campbells came back. This time the castle did not hold. The walls were beaten down and the garrison expelled, and Cairnburgh's military life essentially ended. What survives today are the foundations and lower walls of the barrack block, the chapel, the guard-houses on both islands, and the well, all on uninhabited rocks owned by nobody much, visited by nobody much, dispersed only by gulls.