The church has a long 13thc chancel, a tall chancel arch, two arcades, and a large 15thc W tower. The impressive medieval choir stalls inside come from the nearby Cistercian abbey, founded in 1296. The S door has what appears to be reused Romanesque material.

Whalley appears in Domesday as a significant site: with 87 taxable carucates of land, and two churches. The 1291 Taxatio reveals that it was relatively wealthy, the rectory assessed £66, 13s, 4d (100 marks), due to the large size of the parish, and its five recorded chapelries. The church may have been a former minster, attested by the numerous Anglo-Saxon fragments in the church masonry and the three spectacular crosses in the churchyard from around the year 1000.

The vestry E doorway is mentioned in The Buildings of England as possibly Romanesque. It is a plain round arch, and does not seem to be ancient: the vestry is modern.