The town owes its origin to a sixth-century monastic settlement founded by Saint Molua, or Lua, on an island in the Shannon 1 km below the present Killaloe Bridge which later moved onto the mainland. In the tenth century it was base for Brian Boru as it controlled the strategic crossing of the Shannon above Limerick, where the Vikings were in control. Brian Boru had his palace, Kincora (Ceann Coradh), on the high ground where the current Catholic church stands. Therefore, between 1002 and 1014, when he was the High King, Killaloe was effectively the capital of all Ireland. 2 km north of the town, his fort, Beal Boruma, stood on the site of an Iron Age ring at the head of Lough Derg, where a ford crossed the river. The word “Boruma” comes from the tribute paid by those crossing the river and is thought to be the origin of Brian Boru’s name.
St Flannan’s Cathedral (Church of Ireland) was built between 1185 and 1225, with an oratory for the same saint, who had been the abbot of Killaloe in the seventh century. The cathedral was destroyed and rebuilt in the fourteenth century. Of the original building, only a romanesque arch survives. In Elizabethan times, Ennis was chosen as the county town of Clare, and the importance of Killaloe declined.
In 1650, Cromwell spent 10 days on the opposite side of the Shannon at Ballina, exploring ways to cross the river, which was the defensive line of catholic and royalist forces before the Siege of Limerick. 40 years later, Patrick Sarsfield was the leader of the Jacobite forces here, harrying the Williamite forces advancing on Limerick.