The area surrounding the vicinity of the church has a somewhat complex history. At the time of the Doomsday Survey, there were two distinct villages called Kirkby and Fleetham, both belonging to Alan of Brittany. The name Kirkby derives from the old Norse for ‘a village with a church’. There were two manors at Fleethan, which were held separately until 1086. Subsequently, the lands around both villages seems to have changed hands frequently and not without disputation. The church is situated adjacent to Kirkby Hall and is all that remains of the village of Kirkby, which appears to have become gradually depopulated. A Leonard Smelt, the Northallerton MP, was described on his death in 1740 as ‘of Kirkby Fleetham’, indicating that the villages had been united by this time.
The Domesday Survey records that in 1066 the 'Cherchebi' had a church and a priest. The manor was held by Gamal, son of Karli, and Uhtred; in 1086 it passed under the lordship of Odo the Chamberlain, being the Count Alan of Brittany tenant-in-chief. The manor valued £2.