The present church is essentially of late medieval date; there is no evidence for a church on the site before the 12th century. A Romanesque doorway survived as the N nave entrance until 1797/8 but is now known only from an engraving. Just one carved stone, a scallop capital, appears to have survived from the first church. Another stone, sculpted with a head and leaves, has been by some attributed to the 12th-century, but it is actually of later date. It was found in 1981 during excavations in the S choir aisle, in the foundations under the E wall. A head boss at the W end of the choir vault has also occasionally been mentioned, but again it is of later medieval date. Several changes to the church and various restorations were undertaken after the medieval period, culminating with a major re-organisation of the interior in the years 1872-83 and the addition of the Thistle Chapel in 1910-11.

The Burgh of Edinburgh seems to have been established in the 1120s, but no surviving reference to the church of St Giles has been found before 1178. There was a consecration of the church in 1243. Then, during the 14th century the church suffered severe damage through attacks by Kings Edward II, Edward III and Richard II. However, a contract in 1387 stated that five new chapels were to be built. Thereafter, there is frequent mention of constructional changes to the church.

It has been argued by some that the church of St Giles would not have been built before the founding of the Burgh, probably by King David I, sometime during the 1120s. The first mention of the church in 1178 must surely be a terminus ante quem. The most important evidence for the date of the church seems to be the now-lost N doorway, which has clear stylistic associations with Dalmeny Church (W. Lothian), which is in turn influenced by Dunfermline Abbey Church, started in or soon after 1128. This suggests a date for the Romanesque church of St Giles in the 2nd or 3rd quarters of the 12th century.