Stainton was an Anglo-Saxon settlement and a village by the time of the Norman Conquest. The present church was begun in Norman times and its oldest feature is the Norman north door into the vestry and was enlarged in 1300.
Little history remains on record of St Andrew's church. It may be inferred that this church was destroyed or allowed to fall into decay; during the outbreak of the Civil War the chancel of the church was still standing, but in 1707, when the churchwardens were directed to repair the church and churchyard, there is no mention of the chancel.
In 1718 the church had so fallen on evil days that it even contained 'no altar' and the 'communion cloth' which was there in 1707 had disappeared. By 1846, however, the church was described as being "in good order" and further restorations, of the interior in 1886 and the roof, vestry, east wall and window in 1913, created the church as it appears today, at about a third of its original size.