Nave and chancel church. The nave (length 10.65 m x width 6 m) appears to be of 12thc. date. It is rubble built and raised on a plinth. The plinth, W door and S window are of local dressed sandstone. The chancel (length 6.07m x width c.4.5m) is a later addition, probably of the first quarter of the 13thc. Externally the walls rise from a chamfered plinth and are faced with squared coursed sandstone. Internally the wall facing is of coursed rubble. A sacristy was added to the east end of the church, probably during the 15thc., by the insertion of a cross-wall running the width of the chancel. In the graveyard, close to the church is a tomb or 'mortuary house'. This appears to be contemporary with the chancel, and may have been constructed to accommodate the movement of the founder's tomb from the E end of the original single cell church following its enlargement.

The original E window was demolished when a sacristy was added to the E end in the 15thc. Historical accounts and fragments recovered through excavation suggest a triple pointed lancet arrangement (see Waterman, 1976, 33).

Repairs to the fabric of the church were made in 1883, 1926 and 1972–3 when archaeological investigations were carried out.

Local tradition views the ecclesiastical site at Banagher as a Patrician foundation, however, the earliest known written reference to a church at Banagher is in 1121, when it is recorded that 'Gilla- Epscoip- Eogain Ua Andiaraidh, king of Ciannachta, was killed by his own kinsmen in the centre of the cemetery at Bennchar' (Annals of Ulster, 105). The church was traditionally founded by St Muiredach O'Heney who may have lived in the 11th or 12thc. If the church was the first to be built on the site it is unclear whether it was founded under the old monastic regime, or as a parish church under the fledgling reform movement. By 1306 it is recorded as a parish church in the ecclesiastical taxation (CDI 1302–1307). It was the medieval parish church chosen by Archbishop Colton of Armagh as the base for his visitation of Derry diocese in 1397. It had been abandoned by the 17thc., and was vested in the care of the Commissioners of Public Works in Ireland in 1880.

The peculiar form of the door, lintelled without and arched within, finds its closest parallels with the W doorway of the church at Aghowle, Co. Wicklow and Maghera, Co. Derry. A twin of the SW window is found at Dungiven, two miles to the north. The continuous mouldings of the chancel windows suggest parallels with the so-called School of the West. Mortuary houses similar to that at Banagher occur at nearby Bovevagh, at Clones, Co. Monaghan, and Saul Co. Down.