There was a church at Walton from at least the twelfth century. It was originally a chapel of ease within the parish of Thorp Arch and was given to Nun Monkton Priory at an early date and later appropriated, with its mother church, to the collegiate Chapel of St Mary and the Holy Angels (also known as St Sepulchre’s) in York.

Parts of the present church, which is dedicated to St Peter, date to the twelfth century, although it was largely rebuilt in the fourteenth. The church was restored in 1891. In 1877 a new organ was installed, made by Foster and Andrews of Hull. The village was owned for many years by the Fairfax family. It later passed to the Lane Fox family of Bramham Park and it was George Lane Fox who funded the 1891 restoration work.

Walton appears to have been a separate parish by at least 1821. In 1977 the benefices of Thorpe Arch and Walton were united.

Today Walton is part of the parish of Lower Wharfe and benefice of Bramham, the latter of which also includes Thorp Arch, Bramham and Boston Spa.