St James' is still a large fenland church even though only the western portion of the church remains standing. The looming, 15thc. W tower is followed by a lingering nine-bay nave with N and S aisles. Bays 1-6 are of the 12thc. and bays 7-9, the three western bays, were added in the 13thc. The clerestory dates to the 15thc. as does the brick N aisle. The N porch was added in the 16thc. The S aisle was rebuilt in stone by James Fowler during his 1871 restoration.

Of the 12thc. church there remains the exterior corbel table of the nave, the six bays of the N and S nave arcade, the E crossing arch, and fragments of bay 1 responds and arches leading into the transept from the N and S aisles. The neo-Romanesque exterior S doorway, in the eastern bay of the S aisle, is completely of the 19thc. restoration.

In the Domesday Survey, Freiston is mentioned as one of three 'hundreds' attached to the land of Robert of Vessey in Caythorpe. Within these portions of land were two churches and two priests; so it is possible that Freiston had a church as early as 1086. St. James was given by Alan de Creun (Croun) to the Benedictines at Crowland Abbey in 1114. Sometime after that Freiston Priory of St. James was founded by the monks of Crowland; it continued in existence until 1539 when it was dissolved.

The exterior S doorway is completely renewed, part of Fowler’s 1871 rebuilding of the S aisle. It is not possible to determine the accuracy of this rebuilding. However, the capitals are very similar to the good 12thc. capitals on the S priest's doorway at the neighboring church of Fishtoft, St. Guthlac. Perhaps Fowler used these as his model. The undulating corbel table of the exterior nave walls is the same type as that found at St. Swithin, Bicker (nave), St. Martin, Ancaster (chancel), and Holy Trinity, Allington (bellcote). The fact that it extends for the entire length of the nave should raise a question about its authenticity when one considers the 13thc. lengthening of the nave by three bays, the 15thc. date of the clerestory, and the exterior work by Fowler. The carving on the N side looks crisp and more recent than the worn S side. The central capitals and imposts of the W crossing arch have sharper edges than their counterparts to the W; are they perhaps inserts from Fowler's 1871 restoration?