This is the third Pukekaraka presbytery to be built on this site, since the arrival of Catholic Missionaries to the Kapiti District in 1844. The first presbytery was a simple whare built about 1846 on the hilltop at Pukekaraka for Father Jean Baptiste Comte. Services were held in another raupo structure. When the latter was destroyed by fire in 1856, the community built the existing St Mary's (registered Category I by the New Zealand Historic Places Trust/Pouhere Taonga). By then a large Maori kainga (settlement) had grown around the mission. This kainga was noted for its success with European-style agriculture. It supplied the Wellington market with produce and had its own mill. It was also noted for its support of the Kingitanga movement. The original presbytery was not replaced until 1870 when a timber house was built behind the church. The present presbytery was constructed in 1897during the ministry of Father Francis Melu.

Although this building has been repaired and extended, its appearance is substantially unaltered from when it was first built. It is a large wooden, two-storey building, with a hipped corrugated iron roof. It has an unusual verandah on the front facade, with a triple sunburst motif under the first floor balcony.

The presbytery is situated in a complex of historic structures including St Mary's Church, meeting houses, way of the cross, shrines etc. Today Pukekaraka retains its close connection to the Maori community, although the parish it serves has expanded to include others from the wider community.