Unusually for the Northern Isles, it has been suggested that Egilsay may have a partly Gaelic name. While at first sight, it appears to be Egil's island, "Egil" being a Norse personal name, the Gaelic eaglais (Celtic "eccles") meaning church, may be part of the root, as the island is dominated by a church of pre-Norse foundation. The island of Kili Holm just to the north, may represent cille, a monastic cell.
St Magnus Church has an unusual Irish style round tower, which itself is rare in Scotland, and is unique in Orkney (though other examples are known to have existed in the past). The building is roofless and the tower has been slightly truncated, but it is otherwise complete. It is maintained by Historic Scotland as an Ancient Monument and Category A listed building.
Egilsay was the place where Saint Magnus was killed in 1117 by an axe blow to the head. While the church is dedicated to him, the foundation may be far older. For hundreds of years the story of St. Magnus, part of the Orkneyinga saga, was considered just a legend until a skull with a large crack in it, such as it had been stricken by an axe, was found in the walls of St. Magnus Cathedral in Kirkwall.
The island's population was 26 as recorded by the 2011 census a drop of almost a third since 2001 when there were 37 usual residents. During the same period Scottish island populations as a whole grew by 4% to 103,702.