The tower and the roofless rectangular nave are visible enough, but the older story buried beneath the site is not. No surface trace survives of the medieval parish church of Cúil-Ó-dTaidhg, the settlement whose name, meaning roughly "the retreat of the Tadhgs", was eventually replaced by the more descriptive Baile na hEaglaise, the townland of the church. The two layers of history sit on the same ground without acknowledging each other.

The medieval church here was recorded as early as 1302, when the papal taxation of the Deanery of Offeria in the diocese of Ardfert listed it under a corrupted form of its name and valued it at 13 shillings and 4 pence annually. What makes its administrative history particularly tangled is that the revenues of the parish were not managed locally. An arrangement had developed by which the abbot of O'Dorney monastery in Kerry, a Cistercian house, collected the tithes on behalf of an Augustinian house far away, the monastery of St Mary at Connall in County Kildare, which held the rectorship and received one mark sterling a year from both this parish and the neighbouring parish of Duagh. By 1466 that arrangement had broken down. A papal letter addressed to the abbot of Ratoo, another Kerry monastery, describes how a Kerry cleric named Maurice Fitzmaurice had withheld the tithes, refusing to pass on the pension to Connall abbey. Edmund, abbot of O'Dorney, petitioned Rome to have the fruits of the parish assigned to him for life on the understanding that he, better placed to deal with the "powerful" Fitzmaurice, would recover the revenues and resume the annual payment. The parish then passed through the hands of the Stack family of Ardfert: David Stack held the vicarage until his death in 1479, after which it was granted to his brother Philip, who was at that point Bishop of Ardfert. By 1756, when the antiquary Charles Smith was surveying Kerry's parishes, the church at Ballynahaglish was recorded as vicarial and in repair, with Sir Thomas Denny as patron.

The present ruins are those of a Church of Ireland building. Samuel Lewis, writing in 1837, described it as an ancient structure built in 1619 and situated on an eminence, repaired in 1820 with a grant of £900 from the Board of First Fruits, the ecclesiastical body that funded Protestant church construction and repair in Ireland during the eighteenth and early nineteenth centuries. The National Inventory of Architectural Heritage dates the church itself to 1691, with the three-stage western tower added or reconfigured by 1798. The building was closed in 1894 and dismantled in 1910, leaving the shell that stands today in the graveyard on Church-hill.