In the 16thc, the parish of Deerness was united with the parish of St Andrews W of it. The medieval parish church of Skaill in Deerness was taken down and rebuilt in late 1790s on a new site about 40 feet NW of the earlier church. The last of the foundations of the earlier church were removed in the 1870s. The present church is the 1790s church, remodelled in the 20thc. The medieval church of Skaill was described and drawn by George Low in 1773/4, who said that the chancel was vaulted and that there was another room above this. The church was unusual in that it had two round towers flanking the E end. A coped grave cover carved with tegulation was located until at least 1930 in the NE corner of the graveyard. By 1946, it had been the moved inside into the Session House, where it remains.

King Sigurd of Norway is said to have converted Orkney around 996 AD, but it does not appear to have come under the control of the Roman church until the time of Adalbert, Archbishop of Hamburg (1043-72), who ordained a bishop named Thorulf, probably a missionary bishop, as a result of petition by Iceland, Greenland and Orkney. In 1152/3, Nidaros (Trondheim) became an archbishopric and Orkney came under its ecclesiastical control. Thorkel, foster father of Thorfinn Sigurdsson (died c. 1165) had a homestead in Deerness. An important man under Thorfinn, Thorkel was still alive in 1046 when, according to the Orkney Saga, he killed Rognvald. The date of his own death is, however, unknown. Excavations have uncovered a Norse settlement a short distance N of Skaill church graveyard. A pictish stone has also been found, confirming that the site has a long settlement history. That there was a medieval church at Skaill in Deerness is attested by George Low’s drawing of the church, made in 1773/74.

The coped grave cover bears close comparison with that found at St Magnus Cathedral in Kirkwall (see: Tankerness Museum, Kirkwall). A similarly tiled section of grave cover can also be seen in the Borders region of Scotland in the church at Bedrule (see: Bedrule, Scottish Borders). George Low included a drawing in his 1774 volume which is either that from Skaill in Deerness or that from Rendall, stating that both were similarly carved. Next to the drawing, he specifically labelled it, 'S Tammis', which is the name St Thomas’ Ch. at Rendall was locally called. Despite this, some writers have suggested that the drawing is a depiction of the one at Skaill and not the one at Rendall. Low also stated that the grave cover at Skaill was plain on one side and carved on the other, which does not match with the grave cover preserved in the Session’s House. There is clearly some confusion, but unless the Rendall grave cover is found, it is unlikely that this will be clarified. Gough (1786) copied what Low described, but he is unlikely to have seen the grave cover himself other than as a drawing/print. Lang (1975) has suggested a late-11th or early-12thc date. Neither of the medieval churches at Skaill and Rendall survives, but dating suggestions from drawings (Skaill) and excavations (Rendall) have led scholars to suggest dates in the 12thc for both.