The medieval nave and its crossing tower survive more or less intact to the south of the town centre, while the chancel they once opened onto was demolished in 1827 to make way for a Church of Ireland building, later largely rebuilt in 1872 by the architect Thomas Henry Wyatt. That Victorian church has since fallen out of use in its turn, and the former chancel space now functions as a display room for the medieval stonework the broader site has accumulated over the centuries, including an ogham stone, a collection of graveslabs, and a number of effigial tombs. The medieval font, however, is gone; it was moved to the Church of Ireland at Old Leighlin in Co. Carlow around 1970.

The church's origins reach back into the thirteenth century. Theobald fitz Walter, who died in 1206, granted a charter to the burgesses of what was then called Balligaueran, and it was possibly he who first assigned a portion of the church's rectory to the Knights Templars of the Priory of Kilmainham, who were recorded in possession of it by 1254. By 1312 the advowson, meaning the right to the income and appointments of a church benefice, was the subject of a dispute between Edmund Butler, Earl of Carrick, and the Dean and Chapter of St Canice's Cathedral in Kilkenny. The settlement required the cathedral to maintain four priests to say masses for Butler and his descendants in perpetuity. A collegiate residence for those priests, marked as "Colledge" on a 1710 map of Gowran, adjoined the old churchyard to the east; its foundations were still traceable when the historian Carrigan wrote in 1905. Edmund Butler himself died in London in 1321 and was brought back to be buried here. His son James, the 1st Earl of Ormond, followed him in 1337, and the 3rd Earl, also named James, in 1404. In 1501 the portreeve and commons of the town wrote to the then Earl of Ormond asking him to send ornaments to the church in honour of God and in memory of his noble ancestors buried within it. The architectural history of the building is equally layered. Scholarly analysis of the stonework, particularly the quatrefoil nave piers, the clerestorey windows, and the elaborate dog-tooth ornamentation of the eastern aisle windows, has led to the suggestion that Gowran, St Canice's Cathedral, and St Mary's in Thomastown were all built around 1260 by the same craftsman, referred to in the literature as the "Gowran master".

The surviving nave is the place to spend time. The north arcade remains standing, its quatrefoil piers and chamfered arches largely intact, while the south arcade, still visible in Francis Grose's engraving of 1791, has since collapsed entirely. Two of the four clerestorey windows in the north wall are blocked. The crossing tower, probably heightened in the fifteenth century, had its vaulting removed during the 1872 rebuilding works, and the original tower arch is now visible only as a blocked opening in the west wall, with a thirteenth-century doorway inserted into it and a modern pointed entrance cut into that in turn. In the south aisle, cinquefoil arches frame tomb recesses in the wall, and a double piscina, a shallow wall basin used for rinsing liturgical vessels, survives at the eastern end, missing its central pillar but otherwise legible. A mortuary chapel added by the Kealy family in the seventeenth century contains a wall monument to Piers Kealy and his wife, dated 1648, and a second monument in the north aisle commemorates James Kealy and his two wives, dated 1626.