Of ecclesiastic origin, this is a name derived from the gaelic Macaphersein, meaning "Son of the Parson". The clan itself is reputed to have been founded by Murdo Cattenach, a priest of Kingussie in Badenoch.

The MacPhersons formed part of the great Clan Chattan, and frequently disputed the leadership of this federation with the MacKintosh family. They finally did acknowledge the MacKintosh claim to "Captain of Clan Chattan", but showed them little loyalty in the ensuing years.