That quiet continuity, a medieval baptismal vessel carried forward through dissolution, decay, and eventual rebuilding, is perhaps the most telling detail about the layered ecclesiastical history on this site in Co. Meath.

The place name Dunboyne derives from the Irish Dún Buí, thought to mean the fort of the yellow river, though the small stream that runs near the site has no recorded name. The territorial history here moves quickly through familiar Norman hands. Hugh de Lacy granted the lands of Dunboyne to the Petit family in 1172, and in 1227 Ralph Petit, by then bishop of Meath, endowed a newly founded Augustinian priory at Mullingar with the large parish of Dunboyne among other properties. Early in the fourteenth century, Thomas Butler, a brother of the first Earl of Ormonde, acquired the land through his marriage to Sinolda, the Petit heiress. By the time of the Civil Survey of 1654 to 1656, neither Butlers nor Petits were listed among the local landowners, though the rectory had remained in the abbey's possession until its suppression in 1540. The church itself was clearly substantial: in the ecclesiastical taxation of Pope Nicholas IV, compiled between 1302 and 1306, it was assessed at 40 marks, making it the second wealthiest in the deanery after Ratoath. By 1622 James Ussher still called it a great parish church, but the building was already ruinous. Visitations in the 1680s and 1690s found the church of SS Peter and Paul reduced to standing walls, the chancel patched up with slates and glazed windows but with a clay floor. That chancel remained in use until the present church was built in 1866.

What survives of the medieval structure is a west tower, now heavily obscured by ivy and made inaccessible, with its ground floor vault collapsed and buried. The first floor retains a single-light ogee-headed window, a blocked doorway that once connected to a nave gallery, and a fireplace in the south wall. A newel stair at the south-east angle once gave access to upper floors, which are similarly unreachable today. Wall footings of the north-east angle of the nave extend roughly 33 metres east to west. Architectural fragments preserved in the porch of the current church point to a fifteenth or sixteenth-century date for much of the fabric. The octagonal 1579 font, with its inscription in false relief running across four of its upper panels, sits inside the present church still doing what it was made to do. A second, plainer rectangular font with chamfered angles also survives in the porch, its form shifting from near-octagonal at the top to circular at the base.