The first, consecrated in 1813, was a replacement for a church of St Mary that was founded in 669 within the remains of the Roman fort at Reculver, about 1.25 miles (2 km) to the north-east, but was mostly demolished in 1809.

The first church at Hillborough was poorly constructed, and was itself replaced by the present structure, designed by Joseph Clarke in the Gothic Revival style.

[1] Having stood for about 1,150 years and undergone much enlargement and embellishment, that church was mostly demolished with gunpowder in 1809 at the instigation of the then vicar, Christopher Naylor, partly because it had been at imminent risk of being washed away by the sea through coastal erosion.

[2][3][Fn 1] Further, the settlement that it once served had already been greatly diminished largely by the same process, and its displaced inhabitants had moved to Hillborough, about 1.25 miles (2 km) to the south-west.

[15][Fn 2] On 28 April 1874, when R. H. Blakey was inducted as vicar, the hope was expressed that "a new church may some day be erected which will in every way be more suited for the solemn uses of public worship.

[19][20][12] Costing £1,400 to build, the new church was consecrated on 12 June 1878 in the presence of Edward Parry, Bishop of Dover, who noted in his address to the congregation that it carried a remaining debt of about £200.

[22] Built in the Gothic Revival style, the Church of St Mary the Virgin is faced on the exterior with knapped flint, and has limestone dressings, for example forming the apertures for its lancet windows and at its corners.

[12] An extension comprising a vestry of similar external appearance to the rest of the church, apart from a flat roof and rectangular windows, was added to the southern side of the chancel in 1963.

[19][Fn 6] The church is surrounded by a graveyard, at the northern edge of which a war memorial stands facing into the adjacent Reculver Lane.