The original church on the site—a small wattle and daub structure, later succeeded by a wooden church occupied a pre-Christian site of pagan worship. St Giles' Church "may be one of the best examples of re-use of an old religious site" which was a common practice in Sussex. The present building, like its wooden and wattle and daub predecessors, stands within a stone circle which can still be seen in places, and which probably contained a pagan temple. This may also explain its unusual orientation, northeast–southwest rather than the conventional east–west: the original pre-Christian structures on the site would have been aligned in this way so they would face the sunrise at the summer solstice.

Although the timber church would have existed at the time of the Domesday survey in 1086, it was not recorded in it; only the village was. The absence of church records from the survey was common, though, as its main purpose was to record landholdings for taxation purposes. By this time, a stone-built Saxon church would have been in place; Ralph de Cahaignes possibly ordered its construction to replace the old wooden building. After the Norman conquest, many Sussex churches were rebuilt in Norman style, although Saxon fabric was sometimes retained, and this happened at Horsted Keynes. One doorway and the foot of the tower survive from the Saxon era; the doorway has been repositioned in the north aisle.
In place of the Saxon building, the Normans constructed a large cruciform church with a central tower and tall, sharp spire which forms a landmark for miles around despite the church standing in a dip. The four arms of the cross were formed by the nave, the chancel and a north and south transept.[14] The chancel had an apse and a narrow chancel arch. About 1220, the apse was removed and the chancel rebuilt with a square end and a longer floorplan. Lancet windows were installed, including a large triple window in the new east end. The south transept was also reconstructed and given lancets. The old transept must have been smaller and lower, more like a porch, because the low original 12th-century arches leading to the crossing were retained. The tower is topped with a landmark spire.
Between 1320 and 1330, a new wider chancel arch was installed between the crossing and the chancel, a side chapel was added on the north side, new windows were added in the nave, and the original rounded west arch of the crossing (into the nave) was replaced by a new pointed arch. The side chapel probably replaced the old north transept, which was removed although its roofline can still be traced. One contemporary feature that has now disappeared was a chantry chapel dedicated to Marie de Bradehurst. It was built alongside the chancel and was latterly used as a schoolroom until it was removed in the Victorian era. The dedication relates to the Broadhurst manor in Horsted Keynes parish. The demolition of the chapel revealed the outline of a wide blocked pointed arch on the south wall, which is still clearly visible.

Later work included the reconstruction of the porch at the southwest corner—dated to the late 17th century—and reinforcement of the tower and the west walls of the nave, necessitated by the subsidence of the tower caused by the removal in the 14th century of its north transept and its original rounded west arch. The tower started to lean, and its tall spire accentuated the problem. Buttresses were added in four places, and iron ties were inserted later to bring the tower back towards the vertical. The spire is known to have been in place by 1667, when lightning struck it and dislodged 3,000 shingles.