The first ecclesiastical record of the see is in a papal bull of Pope Adrian IV (1157), confirming to Bishop Edward the churches of Aberdeen and Saint Machar, with the town of Old Aberdeen and other lands.

The see was transferred to Old Aberdeen about 1125, and continued there until 1577, having had in that time a list of twenty-nine bishops.

On 4 March 1878, Pope Leo XIII restored the hierarchy of Scotland by the Bull Ex supremo Apostolatus apice and Vicar-Apostolic John MacDonald was translated to the restored See of Aberdeen as its first bishop.

The Bull made Aberdeen one of the four suffragan sees of the Archdiocese of St. Andrews and Edinburgh, and defined as its territory "the counties of Aberdeen, Kincardine, Banff, Elgin or Moray, Nairn, Ross (except Lewis in the Hebrides), Cromarty, Sutherland, Caithness, the Orkney and Shetland Islands, and that portion of Inverness which lies to the north of a straight line drawn from the most northerly point of Loch Luing to the eastern boundary of the said county of Inverness, where the counties of Aberdeen and Banff join."

In area the diocese is 29,068 square kilometres (11,223 sq mi) approximately one fifth of the land mass of Scotland.