Although first inhabited around the 6th century, the first fortified castle was built in the mid 13th century and stood guard over the lands of Kintail. By the late 13th century it had become a stronghold of the Mackenzies of Kintail (later the Earls of Seaforth). At least four different versions of the castle have been built and re-built on the site.
The name Eilean Donan, or island of Donan, is most probably called after the 6th century Irish Saint, Bishop Donan who came to Scotland around 580 AD. There are several churches dedicated to Donan in the area, and it is likely that he formed a small cell, or community on the island during the late 7th century.
The first fortified structure was not built on the island until the early 13th century as a defensive measure, protecting the lands of Kintail against the Vikings who raided, settled and controlled much of the North of Scotland and the Western Isles between 800 and 1266.
From the mid 13th century, this area was part of the " Sea Kingdom" of the Lords of the Isles. In this kingdom the sea was the main highway and the power of clan chiefs was counted by the number of men and galleys or "birlinns" at their disposal. Eilean Donan offered the perfect defensive position.
Over the centuries, the castle itself has expanded and contracted in size. The medieval castle was probably the largest, with towers and a curtain wall that encompassed nearly the entire island. The main keep stood on the island’s highest point.
Around the end of the 14th century the area of the castle was reduced to about a fifth of its original size, and although the reason is unclear, it probably corresponds to the number of men required to defend the structure.
In 1511, the Macraes, as protectors of the Mackenzies, became the hereditary Constables of the Castle.
In 1539 Iain Dubh Matheson, chief of the Clan Matheson, died whilst defending the castle on Eilean Donan island against the Clan MacDonald of Sleat on behalf of Clan Macrae and Clan Mackenzie.
By the 16th century a hornwork was added to the east wall to offer a firing platform for the newly introduced cannon.