Naburn was a chapelry within the parish of St George, York, until 1586, and then within the united parish of St George’s and St Denys’s, York, although part of the village also lay within the parish of Acaster Malbis. In 1842 it was made a parish in its own right. At this time the parishioners were served by the chapel of St Nicholas in the grounds of Naburn Hall.
The advowson belonged to the Palmes family of Naburn Hall from 1842 until 1911, when it passed to the Archbishop of York. In 1951 the vicarage of Naburn was united with that of Stillingfleet. The parish church of St Matthew the Apostle was erected in 1853-1854 to a design by George Townsend Andrews. It was renovated and reopened in 1889, with the addition of an organ and new choir stalls, as well as an oak screen and stained-glass windows by J. W. Knowles of York.
A churchyard was consecrated there in 1854 and extended in 1905. Prior to this date, parishioners had been buried at St George’s churchyard in York or at Acaster Malbis. There was also a parsonage house in Naburn by the eighteenth century. It was replaced by a new brick vicarage in 1877.
The church required substantial renovations by the late 1980s and was briefly declared redundant when funding could not be found. However, an appeal was launched by parishioners and the church was restored and rededicated by the Archbishop of York in 1999.
Today the parish is part of the benefice of Escrick and Stillingfleet with Naburn and together with the Derwent Ings Benefice form the Rivers Partnership of 8 churches.