The window that once occupied the centre of that west wall has been broken out entirely, and a modern concrete buttress props up the southern end of the surviving masonry. The north, south, and east walls have disappeared below ground. A roughly square graveyard still surrounds the ruin, and possible earthworks have been noted just beyond its outer wall, hinting that the site's footprint was once larger than what is visible today.

The church's documentary trail is surprisingly detailed for a place so reduced. By 1540 to 1541 it appeared in records as the rectory of 'Kylsen, among the Irish', listed as part of the estate of the Hospitallers of Kilmainham, the Irish branch of the Knights of St John of Jerusalem, a military-religious order that held substantial Irish properties until the dissolution of the monasteries. At that point the rectory was being farmed by one Charles Rowe O Connor, who owed four pounds but was paying nothing. A decade later it was described as the 'parsonage of Balnekill', still tied to the Kilmainham priory, and it was significant enough to be marked on the 1563 map of Laois-Offaly. In 1609 King James I granted the church and its tithes, along with lands spread across a remarkable list of townlands, to Francis Gofton, one of the auditors of the imprests in England. The grant also included the glebe land at Ballinrath and the advowson of the vicarage, meaning the right to appoint its priest. By the Civil Survey of 1654 to 1656 the lands of Ballynakill belonged to a Protestant landowner named Richard Aprice, whose title was confirmed again in 1660 alongside a John Sankey. The Ordnance Survey's six-inch map of 1838 still showed the ruins standing at the centre of their graveyard; by the revised twenty-five-inch edition of 1908, only the west gable and a short return of the north wall were recorded as upstanding. The slow erasure was already well advanced.