Stockton on the Forest was a chapelry within the parish and Prebend of Bugthorpe until 1738 when it was augmented through Queen Anne’s Bounty and became a separate ecclesiastical parish. It remained subject to the peculiar jurisdiction of the Prebend of Bugthorpe however until the nineteenth century. In 1840 the advowson of the church was transferred from the Prebend to the Archbishop of York.

The earliest reference to a chapel at Stockton was in 1276. The medieval building was demolished in 1808 and replaced by a new church. This was partially rebuilt in 1843 and then more substantially rebuilt in 1895 by architects Naylor and Sale of Derby, retaining the earlier nave but adding a new chancel, tower, clergy and choir vestries and an organ chamber. The church is dedicated to the Holy Trinity.

In 1939 Stockton on the Forest became the mother church of Warthill and Holtby parishes following the union of the three benefices. An alteration to the boundaries with Huntington took place on the 23rd August 1967.

Since 2012 Stockton on the Forest has been part of the benefice of Rural East York, which also includes Dunnington, Holtby and Warthill.