At the eastern end of the nave, a two-storey tower house was built directly onto the chancel, blurring the line between a place of worship and a fortified residence. A tower house is a compact, defensible stone structure common across medieval Ireland, typically associated with secular lords rather than liturgical architecture. Here, the two uses were merged into a single building, and the internal arrangements still hint at that arrangement: a mural staircase, set within the thickness of the wall, connected the ground level to a first-floor residential space, while a further stair and passage ran across the western wall of the tower, probably leading to a second storey above. The west gable of the church retains a single round-headed window at first-floor level, its bar holes still visible, and the base of a medieval baptismal font sits near the west end.

By 1622, when a formal visitation of the Diocese of Meath was carried out, the building was already old enough to require attention. The visitation recorded that the church and chancel had been repaired, and noted the presence of 'a small castle at the east end of the Chauncell', confirming that the fortified attachment was a recognised feature rather than a later anomaly. At that time the rectory was under the patronage of the Lord Viscount of Drogheda, and the incumbent minister was one James Byram, described in the record as a 'preaching minister'. When the antiquary Cogan wrote about the site in the 1860s, the bell-tower on the north side of the sanctuary was still standing to a considerable height, and he recorded the church's dimensions as approximately seventy feet by twenty-two, along with a baptismal font whose bowl measured one foot six inches across. The motte and bailey earthworks of an earlier castle complex, a form of Norman fortification consisting of a raised earthen mound beside an enclosed courtyard, lie roughly eighty-five metres to the northwest, suggesting that Rathconnell was a place of some strategic and ecclesiastical significance over several centuries.

The ruins sit within a graveyard in open pasture, and the ivy-covered walls noted in a 1974 survey give a reasonable sense of what a visitor will find. The south wall and west gable are the best-preserved sections; the east gable survives only in traces. The mural staircase in the northwest angle tower and the residential tower at the east end are the features that reward a closer look, offering a concrete sense of how ecclesiastical and domestic space were once made to coexist within a single set of walls.