The Church of Ireland building at Ballymorin, dedicated to St Nicholas, sits in the northern quadrant of its graveyard, and there is good reason to think the ground beneath it has been a place of Christian worship since the medieval period, possibly longer.

The evidence for an earlier structure comes from the Down Survey of 1657, a vast mapping project carried out under William Petty following the Cromwellian conquest, which recorded landholdings across Ireland in considerable detail. The parish map of Ballymorin, held among the manuscripts of the National Library of Ireland, shows a church standing just north of the southern boundary of the glebe land, the plot of ground assigned to support a parish clergyman, with a house depicted a little further south in an area annotated on later Ordnance Survey maps as "Almoritia". The accompanying terrier, a written schedule of lands and features, records plainly that the townland contained a "House and Church". Whether the fabric of that earlier building was entirely cleared away or partly absorbed into what stands today is uncertain, but the possibility that some of the older material survives within the present walls has been noted.

The current building was rebuilt around 1816 in a subdued Gothic style and then altered again around 1887, when a shallow chancel was added to the east end and a single-storey vestry to the northeast corner. The west end carries a three-stage square tower finished with a raised parapet, English-style crenellations, the tooth-like battlements associated with Gothic Revival architecture, and corner pinnacles. Despite the alterations, the building is considered to retain much of its early nineteenth-century character and form.