Over a thousand years before the medieval surveyor marked out the lines of the fortifications that we see today, the vitrified defenses of an earlier fortification encircled the small knoll on the island. Apart from some relic fragments of these early defenses beside the castle walls, the precise line of the earlier fort is buried beneath the castle.

The mediaeval castle was formerly one of the most important strongholds along the western seas. It was built shortly after the Battle of Largs, when the Scandinavian Crown lost title to these shores, reputedly as a base for the heritors of the area, the Earls of Ross, to ensure that it was never again lost to the Scottish Crown. Tradition reports how, though built for the Earls of Ross, by the later 13th century his nephew, Kenneth McKenzie had, through a crushing defeat of his uncle's forces turned his residency into ownership. By the time of Kenneth's death in 1304 the Crown had settled the Barony of Kintail on Kenneth.Tradition relates that Robert the Bruce was given shelter here, but less welcome was the visit by Randolph, Earl of Moray and Warden of all Scotland in 1331. To mark the arrival of this strict disciplinarian, fifty "miscreants" were executed and their heads placed upon the walls of the castle. Greatly pleased, he claimed that the sight of Justice so displayed was sweeter to him than any garland of roses.

The Earldom of Ross continued to press it's claims to the castle, and, in 1350 went so far as to seize the MacKenzie chief (another Kenneth), and execute him at Inverness. Kenneth's heir was quickly dispatched to the Western Isles  until confirmed in his title to the lands by David II. By this time the clan Macrae, destined to be the MacKenzies "Coat of Mail", had settled in the district, followed shortly thereafter by the clan MacLennan.
The first half of the 16th century was a difficult and dangerous time for the MacKenzies and their castle. In 1497 one hector Roy MacKenzie became Tutor (or Guardian) to John, a minor, and had to be dislodged by law after involving the family in feuding with both the Crown and other clans. In 1539 the MacKenzies joined with the MacLeods in disputing Donald Gorm MacDonald of Sleat's claim to the Lordship of the isles. MacDonald sailed with fifty ships to lay siege to the castle, which was occupied at the time only by the Constable, John Dubh Matheson, and a "watchman". Duncan MacRae who was passing as the fleet approached hastened to the aid of the beleaguered pair. The Constable was shot by an arrow and killed, and before long Duncan Macrae was reduced to a single arrow that he resolved to hold onto for the time being. Sensing victory, Donald Gorm MacDonald ordered up a battering ram, and, on passing close to the curtain wall, Duncan Macrae seized his chance and fired the single arrow. It embedded itself deep in the foot of the chief, who in the heat of impending victory impatiently wrenched it out. The sharp barbs severed the artery, and unable to staunch the flow of blood their chief bled to death. With the lifting of the siege Duncan harboured hopes that his action might win him the position of Constable from the grateful Chief. However, the Chief apparently thought otherwise, and in a pique Duncan left the district, after first marrying the widow of John Matheson, the former Constable of Eilean Donan.     
As Earls of Seaforth, the MacKenzies gave their support to the Royalist cause. After the execution of Charles I the Scottish Parliament was sufficiently concerned to impose a garrison at Eilean Donan. They treated the locals very badly, and, as winter advanced, demanded that wood be provided by them. A party of thirty, led by an officer, John Campbell, and Blytheman, his sergeant, set off to enforce their demands. On being met by a deputation of ten locals there to complain, Campbell ordered his men to open fire. No-one was hurt, but passions  were inflamed . Drawing their swords the Kintail men fell upon the soldiers. A single stroke severed Campbell's head, right arm, and shoulder from the rest of his body. Blytheman was killed  at a stream, and several other soldiers  died as the remainder put to flight. In 1645 retribution of a sort occurred when Cromwell's Lieutenant, General Monk, arrived and plundering the district, set houses alight and killed one Duncan Macrae, an old soldier whose death "
by the sword" was said to have been told by Coinneach Odhar.   

During the rising of 1715, Government forces were again stationed in the castle, but were dislodged by the men of Kintail. On the eve of Sherrifmuir a great dance was held on the roof before the men set out to a defeat that was to leave fifty-eight widows in the district. It was about this time that brigadier Louis Petit Des Etans was sent by the government to make a plan of castles in the West Highlands that might be used as centers of disaffection by the Highlanders. In view of what was it happen to the castle within just a few short years of his visit, the plan he made of Eilean Donan is an invaluable record of the later mediaeval works.
In 1719 a foolhardy Jacobite plot was launched to recover the defeat of 1715 that was to result in the destruction of much of the castle.

For two centuries it stood as a picturesque ruin, its history and it's former grandeur embellished by all who passed by. Between 1912 and 1932 it was restored by Farquhar Macrae of Auchtertyre for it's new owner , Lt. Colonel MacRae-Gilstrap. It is said the form of the reconstruction was revealed to farquhar in a dream. It is certainly remarkable that it so faithfully follows what Louis Petit's illustration records, though the latter's drawings were not discovered until long after the reconstruction was complete.