Before any English garrison arrived, the lands around the upper Ilen were O'Donovan country. The O'Donovans were one of the great native families of southwest Munster, descended through the Eoghanachta line that had once supplied kings to Cashel. By the sixteenth century they had divided into several septs - branches of the family with their own territories. The Clann Cathail held this valley. Their original name for the castle was Sowagh; only later did it come to be known as the Castle of O'Donovan, or Castle Donovan, after the Manor of which it was the seat. Donal of the Hides, Lord of Clancahill from around 1560 until his death in 1584, is credited with building or substantially augmenting the tower. His son Donal II carried out further work some decades later, though by then the family had relocated to Rahine Manor on the coast, where Atlantic trade was more profitable than upland farming.

By the late 1640s, the Irish Confederate Wars had been grinding through Munster for years. Donal III O'Donovan had taken the Stuart side, supporting Charles I and his cause; he had also been implicated in the rebellion and massacres of 1641, when the rising of Catholic Irish against settlers and English authority spilled over into the killing of Protestant civilians whose deaths haunted English politics for the next two decades. When Oliver Cromwell's New Model Army swept through Ireland in 1649-50, it carried with it a determination to break the power of Catholic landowners and the strongholds they held. The tradition is that Cromwell's soldiers placed gunpowder against Castle Donovan and blew it up. The damage was specific: a small gouge in the southwest corner, but with deep cracks radiating through the masonry. The tower was left structurally unsafe, and the O'Donovans, who in any case had moved out long before, never returned to live in it.

After the explosion, the tower stood, but its days as a building were finished. The bawn - the surrounding fortified wall - and the outbuildings disappeared into stone-robbed fields. In 1828, a traveller identified only as J.F.W. visited what he called the vale of Castle Donovan and made a drawing that still showed several outbuildings then intact. His account, published in the Dublin Penny Journal in November 1834, captured the place in a phase of its long ruin. The cracks deepened with each century. Eventually, more than two hundred years after the gunpowder, the entire western wall - except for the still-intact spiral staircase tucked inside it - collapsed. Most of the southern wall went with it. What remains today is over two-thirds of the original tower, but the silhouette from certain angles tells the story: the building has lost a face. Between 2001 and 2014, the Office of Public Works carried out conservation work, stabilizing what was left as a listed National Monument. The tower will not fall further. It will not, however, be rebuilt.