The present church was designed by the prolific Wiltshire architect T. H. Wyatt. Its foundation stone was laid in 1841 and the shell of the building was completed in 1847, but the church was not consecrated until 1850. The font, which dates from c.1200, was brought from the medieval church which stood on a different site in the same churchyard.

In 1086, the estate which became Cholderton manor was worth 3½ hides less 4 acres and was held by William of Eu (d. c.1095). The overlordship later descended to Walter Marshal, earl of Pembroke (d. 1245). William's tenant in 1086 was Bernard, and the mesne lordship was passed down in this family to Roger Bernard (fl. c. 1175), and later Eudes Bernard in 1242-43 . By 1242-43, however, the manor had been subinfeudated to the de Argentine family, and further subinfeudated to Alan of Bassingbourn, passing down in the Bassingbourn line into the 14th century (VCH XV, 1995).

There is evidence of a church c. 1175, when Roger Bernard granted it to St Neots' priory. The priory held the advowson until 1337 (VCH XV, 1995).

A 15th century roof was reused in the new church. According to Pevsner & Cherry, this roof was brought from Ipswich by Thomas Mozley, rector from 1836-1846, and installed at a total cost of £6,000. £5,000 of this sum was contributed by Mozley (Pevsner & Cherry 1975, 177).