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Apinayé or Apinajé is not the self-designation of the group, but it is presently the name by which they call themselves and are called by other Timbira groups and by their regional neighbors. In Eastern Timbira vocabulary, the suffix yê/jê designates collectivity.

Curt Nimuendajú provided other names for the group, all of which were derived from the term hôt or hôto among the Eastern Timbira, which means "corner, angle, nook" and refers to the traditional territory of the Apinajé located in the "angle" formed by the Araguaia and Tocantins, a region known as Parrot’s Beak.