The dedication is to Gobán, an early Irish saint, preserved in the Irish form of the place-name, Cill Gobáin. Despite that long continuity, nothing visible survives above ground from the Early Christian period, and the layers of history beneath the present structure have largely been absorbed or erased by successive rebuilds.

The site appears in the Papal Taxation List for the diocese of Ardfert, compiled between 1302 and 1307, which indicates it was a functioning parish church by the medieval period. A Royal Visitation of 1615 found both the church and its chancel to be in good repair, and a note from 1756 confirms the building was still serviceable at that date. It was most likely cleared when the current structure went up in 1824. One striking survival from the earlier building is an oval limestone font, still preserved inside, bearing the inscription W COLLIS RECTOR 1729, a quiet record of a rector who oversaw the parish nearly a century before the present walls were raised. The landscape around the site carries further traces of memory in its place-names: the townland immediately to the west is called Tonakilly, from the Irish Tón na Cille meaning the backside or rear of the church, and a spot on the nearby shore goes by Bunatemple, Bun an Teampaill, meaning the foot or base of the temple. Both names suggest that local usage long mapped the sacred geography of this spot, even when the buildings themselves changed or disappeared.