The history of a church in Allerthorpe dates back at least to the 12th century when sometime between 1100 and 1108 it is recorded that a chapel was given by the king between, along with the mother-church of Pocklington, to the archbishop of York and York minster. Subsequently the chapel was apparently assigned by the archbishop to the dean, and between c.1119 and 1129 the king confirmed the assignment.

In 1252 a vicarage was fully ordained jointly at Thornton and Allerthorpe, with provision that a minister be found for each church. There were separate ministers in 1525-6, but from the 17th century the vicarage and curacy were usually held by one man. Baptisms and marriages apparently took place at Allerthorpe after 1252, but the right of burial was reserved to Pocklington until 1360.

The original church of St. Botolph was small, and consisted of chancel and nave with pedimented bellcot and south porch. In the early 19th century a vestry was added to the north of the chancel. The church was rebuilt in 1876, by Arthur Duncombe, of limestone rubble with ashlar dressings, in a mixture of 14th and 15th century styles; it comprises chancel with north vestry and nave with bellcot and south door. The bellcot is supported by a large corbelled buttress. The church has two bells as it had in 1552.

The churchyard at Allerthorpe, described as the 'ancient' one, was consecrated in 1828 and used thereafter.