Achnacone has a history roughly parallel with that of the neighbouring properties of Invernahyle and Fasnacloich, all clustered together in the southern part of Appin. They were all part of the lands of Dugald Stewart, 3rd of Appin, who gave them to his sons after surviving the disaster of Flodden, 9 September 1513. Each then went on to found a family at those places, of which the Achnacone Stewarts are the last to be in continuous possession to this day. The present house is of somewhat later date and has some modest Victorian additions.

The name is said to mean "the Place of the Dogs" (though this is a little doubtful) and it is conjectured to have been, in James IV's reign, the site of the royal kennels where the king kept his hounds while hunting from Castle Stalker, which can be seen at a little distance westward from Achnacone. The present laird is the 16th to possess Achnacone. Sir Walter Scott is supposed to have visited there whilst staying with his friend, Alexander Stewart, 8th of Invernahyle, on the neighbouring estate; Scott's Oak is still pointed out on the west bank of the River Hyle which divides the two properties.

Two members of the family, Alexander and Duncan, were killed at Culloden, fighting for the Jacobite cause in the Appin Regiment. The Stewart Society was last at Achnacone on 2 September 1979 during the Gathering week-end when Castle Stalker and other neighbouring sites were also visited.