The site takes its name from Cill Gobáin, the church of Gobán, suggesting an Early Christian foundation, though no physical trace of that period survives above ground. What does survive is the surrounding place-name evidence: the townland immediately to the west is called Tón na Cille, meaning the backside or base of the church, and a spot on the nearby shoreline carries the name Bun an Teampaill, the foot of the temple or church. These names tend to outlast the structures that inspired them by centuries, and here they form a kind of ghostly outline around a building that has otherwise left no visible mark.

The site appears in the Papal Taxation List for the diocese of Ardfert, dated 1302 to 1307, which recorded parish churches across Ireland for the purpose of levying a tax to fund crusading efforts. The fact that Kilgobban features in that list confirms its status as an established parish at that point, but the Early Christian origins the name implies remain unverified on the ground. A Royal Visitation of 1615 found both the church and chancel in good condition, and a later account from 1756 noted the building was still in repair. At some point between then and 1824, the earlier structure was most likely demolished to make way for the present edifice. One object bridges the gap between these phases: an oval limestone font, still kept within the church, bearing the inscription W COLLIS RECTOR 1729. Baptismal fonts were often retained even when church buildings were replaced, and this one connects the current structure to a rector who would have served in the pre-1824 building.