Hartley Wintney belonged to the manor of Odiham which, in 1086, had two churches. The advowson of St Mary Magdalene’s in Hartley Wintney was granted to Wintney Priory, a convent of Cistercian nuns founded nearby between 1154 and 1171 (Hare, 2015). Various dates have been suggested for this grant, with the VCH suggesting that St Mary's was part of the original endowment of the Priory. Most authors have assumed that church served the Priory as well as the parish. The Priory’s calendar of prayers records the rebuilding of the church in stone in 1234. This may have been a partial rebuilding, since it has been suggested that the chancel has Anglo-Saxon features (Bullen et al. 2010, 314). Wintney Priory was dissolved in 1536.
Brick transepts designed by William Gover were added to the church in 1834 and the W tower was erected in 1842-43. St Mary’s was superseded by a new parish church dedicated to St John the Evangelist, designed by E. A. Lansdowne, in 1869-70. Thenceforth, the building was used principally for burial services.