Ardfert, in north Kerry, derives from the Irish "Ard Ferta", meaning the height of burial mounds, and the full form, Ard Ferta Brenaind, ties it to St Brendan of Clonfert, the sixth-century navigator-saint. What is stranger still is the gap between those two facts and the evidence: the church is generally regarded as a sixth-century foundation, yet nothing is actually known of its history until the eleventh century, when the annals open with a man named MacMara fasting against Brendan at the site in 1031, and the death of Ailill Ua Flaithim, described as the leading jurist of Munster, recorded the following year. By 1046 the stone church had been struck by lightning and destroyed; by 1089 the whole settlement was burning. This was, at various points, a diocese, a borough, a legal centre with a royal prison, and a place where the justiciar of Ireland held court. Very little of that survives above ground as a coherent whole.

The ecclesiastical and political history of Ardfert is one of repeated destruction and incomplete recovery. The see of Kerry, allocated elsewhere at the Synod of Raith Bressail in 1111, soon settled at Ardfert and remained there throughout the medieval period, though the town was burned in 1152 by O Cuilein, king of Ui Chonaill Gabhra, and again in 1179. In 1180 the Clann Charthaigh plundered it and, according to the annals, killed many senior clergy within their sanctuary and graveyard. Anglo-Norman influence arrived gradually after King John granted north Kerry to Meiler FitzHenry in 1200, and around 1214 to 1215 the Geraldine houses of Desmond and Kerry extended their grip on the region. A Franciscan friary was founded here around 1253, probably by Thomas FitzMaurice, lord of Kerry, and by 1286 the settlement was substantial enough to receive a murage grant, that is, a customs levy collected specifically to fund the building of town walls. A 1293 receipt roll records £8 18s. collected on 44 hogsheads and one pipe of wine; a provost and at least one named burgess, John le Draper, appear in records of the 1290s. Then the Desmond revolt of the late sixteenth century undid much of it. Spanish forces and the earl of Desmond besieged the castle in 1580 and were repulsed; two years later an English garrison was driven out with heavy losses. A 1584 survey found the town and cathedral nearly "prostrated and devastated". The Franciscans were expelled that same year, and the holdings passed to Sir Francis Walsingham, Edward Denny, and other Munster planters in 1587. By 1659 the census recorded a population of 47. In 1687 Sir Richard Cox wrote that it had "of late soe decayd that it contains onely a few Cabbins".

One detail from the domestic record is particularly evocative. A mansion built near the friary by David Crosbie in 1633 to 1635 was marked with a stone inscribed in Latin: the work begun in the year of the Lord 1633, finished in 1635, with the motto "Where there is faith and truth, God will provide". It probably burned in the Confederate wars not long afterwards. In 1645, Edmund FitzMaurice ordered the portreeve and inhabitants to assist in demolishing whatever remained of it. The stone itself was not relocated when later researchers looked for it. A description from around 1682 noted an "infinite deal of stone walls and traces of old foundations", a phrase that still describes the archaeology of the place with some accuracy.