By the time the Ordnance Survey teams passed through in 1841, not a stone of Ballynacourty Church remained above ground. The graveyard outlasted the building entirely, as graveyards so often do in Ireland, continuing to hold the memory of a parish long after the parish itself had reorganised or dissolved around it.

The church has a documented, if fragmentary, history. It appears in the Desmond Inquisition of 1584, a legal survey conducted in the aftermath of the Desmond Rebellions that sought to account for lands and institutions across Munster. By 1622 it was still functioning as a parochial church, recorded in a diocesan list preserved in Trinity College Dublin. Sometime in the following century and a half, it fell away. A 1756 account by the Cork historian Charles Smith noted it already in ruins. What caused the decline is not recorded, but the trajectory, from functioning parish church to rubble to bare ground, follows a pattern familiar across the post-Reformation and post-rebellion landscape of Kerry, where disruption to Catholic ecclesiastical life left many medieval structures without the resources or communities to maintain them.