A church was present on the site at the date of the Domesday Survey,^[3] and it was replaced by a further church in 1530.^[1] By 1827 the chancel of this church had been demolished; at that time it consisted of a west tower and a nave in Perpendicular style.^[4] It was almost completely rebuilt in the middle of the 19th century, the tower in 1848 and the rest of the church between 1852 and 1854.^[1] The new church incorporated some items from the previous churches.^[4] It was designed by the rector at that time, Rev J. H. Sperling.^[5]

The church is constructed in alternating blocks of limestone and knapped flint fieldstone flushwork, forming a chequerboard pattern, and it has a tiled roof.^[1] Its plan consists of a four-bay nave with a north porch, a two-bay chancel with a north vestry, and a west tower. The bays are separated by five-stage buttresses.^[2] The tower is in three stages, with similar buttresses at the angles; it has an embattled parapet with gargoyles at the corners. All the windows are arched with three lights and tracery. Both the porch and the vestry are gabled.^[1] Items reused from former churches include a doorway dating from the 14th century, the tower arch of the 1530 church, and the gargoyles.^[4]

During the 20th century the condition of the church deteriorated and by the 1970s it was largely derelict. It was declared redundant in 1976, deconsecrated, and a demolition order was granted.^[3] However, in 1979 it was taken into the care of the charity the Friends of Friendless Churches.^[4] The charity holds the freehold with effect from 5 December 1979.^[6] By the time it was taken over, tiles had been removed from the roofs, stained glass designed by William Wailes had been removed, and the font was in the churchyard.^[4] The organ dating from about 1860, designed by George Holdich, had also been removed.^[5] During the next few years money was raised for repair and restoration, and the Friends of Papworth St Agnes was founded.^[3][4] One surviving panel of stained glass was moved to the Stained Glass Museum at Ely Cathedral.^[7] As part of the restoration, modern lighting was installed, and a kitchen and toilets were added.^[3] Activities in the church were resumed in 2006, the font was returned to the interior of the church, and the stained glass window was also returned.^[5] The church is now used as a community centre,^[7] and services are occasionally held.^[3]