In April 1647 Murrough O'Brien, the Protestant Baron of Inchiquin replaced Philip Sydney, Lord Lisle as the Parliamentarian Lord-Lieutenant of Ireland as Sydney's one year appointment had by then expired. Because of his Gaelic background O'Brien was not trusted by many Parliamentarians, not least by Lord Lisle, however the latter had achieved little in his time as Lord-Lieutenant and as a result Inchiquin did not need to deal with any serious opposition by the English Parliament.
O'Brien immediately embarked upon a vigorous summer offensive, rapidly capturing Dromana, Cappoquin and Dungarvan in County Waterford to the east. Raiding parties were dispatched northwards against the counties of Limerick and Clare, and Inchiquin next turned his attention to the bountiful County of Tipperary in central Munster. In early September, his forces quickly took the Castle of Cahir. This strong Tipperary castle was well positioned to become a base for the Cork Protestant army, and it was used to raid and devastate the surrounding countryside. The Munster army under Lord Taaffe did not make any serious effort to oppose Inchiquin, probably the result of the political scheming of Muskerry and other powerful Irish lords who hoped to keep the Munster army intact for their own ends. As such, Inchiquin was allowed to make a furthur push eastwards towards the town and ecclesiastical centre of Cashel.
Inchiquin had already launched two minor raids against Cashel, and he now had the opportunity to launch a major assault. The Parliamentarian forces first stormed nearby Roche Castle, putting fifty warders to the sword. This attack terrified the local inhabitants of the region, some of whom fled to hiding places, while hundreds of others fled promptly to the rock of Cashel, a stronger place than the town itself. Lord Taaffe had placed six companies in the fortified churchyard that sat upon the rock, and considered the place defensible, though he did himself did not stay to put it to the test, leaving command to the Governor Lieutenant-Colonel Butler.
Arriving with his army at the Rock, Inchiquin called for surrender within an hour. The defenders of the churchyard offered to negotiate, but that was refused, and on the afternoon of the 15th of September the assault commenced. The Parliamentarians were first reminded of earlier atrocities against Protestants, and then began to deploy. The attack was led by around 150 dismounted horse officers (who wore more armour than the foot) with the remainder of the infantry following; troops of horse rode along the flanks of the advancing force to encourage the infantry. The Irish soldiers attempted to drive off the attackers with pikes while the civilians inside hurled rocks down from the walls: in turn the attackers hurled fire-brands into the compound, setting some of the buildings inside on fire. Although many were wounded, the Parliamentarians gradually fought their way over the walls, pushing the garrison into the church.
Initially, the Irish defenders managed to protect the Church, holding off the attackers trying to get through the doors, but the Parliamentarians then placed numerous ladders against the many windows in the church and swarmed the building. For another half an hour fighting raged inside the church, until the depleted defenders retreated up the bell tower. Only sixty soldiers of the garrison remained at this point, and they thus accepted a call to surrender. However, after they had descended the tower and thrown their swords away, all were killed.
The losses amongst the Parliamentarian soldiers were light. One contemporary states that as few as eight Parliamentarians were killed in the attack, apart from another hundred or so injured.
In the end all the soldiers (save a single major) and most of the civilians on the Rock were killed by the attackers. The Bishop and Mayor of Cashel along with a few others survived by taking shelter in a secret hiding place. Apart from these a few women were spared, after being stripped of their clothes, and a small number of wealthy civilians were taken prisoner, but these were the exceptions. Overall, close to 1,000 were killed, amongst them Lieutenant-Colonel Butler. Theobald Stapleton, a clergyman who in 1639 published the first religious work in the Irish Gaelic language, was another prominent victim of the atrocity. Afterwards, a witness of the slaughter would record that the bodies in the churchyard were in piles five or six deep.
The slaughter was followed by extensive plunder. There was much of value inside, for apart from pictures, chalices and vestments of the church, many of the slain civilians had also brought their valuables with them. The sword and mace of the mayor of Cashel, in addition to the coach of the Bishop were captured. The plunder was accompanied by acts of iconoclasm, with statues smashed and pictures defaced. The deserted town of Cashel was also torched.
The atrocity at Cashel caused a deep impact in Ireland, as it was the worst single atrocity committed in Ireland since the start of fighting in 1641. Previously, the most infamous massacre amongst the Catholic population was that at Timolin in 1643, when 200 civilians were killed by Ormonde's army, but many more than this were killed at Cashel, and this atrocity was compounded by the fact that the Rock of Cashel was one of the chief holy places of Ireland. The political ramifications in the Irish confederation were also profound, serving to exacerbate the split between the Catholic party headed by Rinuccini and those sympathetic to the Royalist lord Ormonde. The former were enraged by the attack, and desired retribution against Inchiquin and his army, but the Ormondist faction saw the Sack of Cashel and a subsequent raid by Inchiquin's men into Kilkenny as evidence of the futility of defending Ireland without Royalist support. Taaffe was subsequently put under intense pressure by the Confederate leadership to engage Inchiquin, but when he did so at the battle of Knocknanauss in November of the same year the Munster army was destroyed. The divisions amongst the Confederates would subsequently exacerbate, leading to the brief but bloody Irish Confederate Civil War in 1648.
Manning, Roger, Oxford (2006), An Apprenticeship in Arms: The Origins of the British Army 1585-1702