A large fenland church which was originally not only larger, but also cruciform in plan with a crossing tower as can be seen in pre-1800 drawings. In 1804-5, the church took on its present form which consists of a six-bay 13thc. nave with side aisles, a 14thc./15thc. clerestory and chancel, and the W tower with flanking N and S bays embracing it. This early 19thc. restoration was done under the direction of William Hayward; at the end of the same century, 1897-1900, C. H. Fowler directed another restoration that focused on the chancel. Surviving from the Romanesque church are the original W doorway of the nave (now within the early 19thc. W tower) and the arch of the S doorway.

Given the name of the village, 'Kirton,' it has been suggested that there may have been an important church here as early as the Scandinavian invasions of the 9thc. and 10thc. (Sawyer, 63). Kirton-in-Holland is listed as 'Cherchetune' hundred in the Domesday Survey which records the existence of a church here in 1086 in the possession of Count Alan.

Above the original W doorway runs a plain chamfered string course which may have extended across the width of the 12thc. façade. Pevsner characterizes the entire W doorway as 'Norman' and the S doorway as having 'Early English' shafts with a reused 'late Norman' arch. However, with the exception of the ring shafts on the S doorway, the capitals and imposts of both the W and S doorways are nearly identical. Also, the central joins in the apex of both arches are slightly misaligned suggesting that both arches have been re-set. In light of this, the 12thc. arches of both doorways may have been re-set when the jambs of both doorways were renewed during the early 13thc. rebuilding of the nave. There is a tradition that the first stone church here was constructed under the patronage of the Bishop Alexander of Lincoln (1123-48). The decorative motifs of the first and third order arches of the S doorway here provide a link with the sculptural program of the W portals at Lincoln Cathedral which have been associated with Bishop Alexander. The use of bobbins on a roll in the first order and the coffered, point-to-point chevron of the third order have parallels in the second and fourth orders of the W front, S doorway at Lincoln Cathedral. Also the use of dogtooth in a hollow chamfer on the first order here can be found the third order of the W front, N doorway at Lincoln Cathedral (though not attached to bobbins).