An apparatus for automatically separating hair follicles includes a follicle separating unit configured to cut a skin tissue of a scalp cut from a back of a head of an alopecic patient in units of follicles and to classify follicles by a number of hairs included in each follicle in an incisional hair transplant or to classify follicles each directly extracted from the back of the head of the alopecic patient by the number of hairs included in each follicle in a non-incisional hair transplant, and a follicle separation control unit configured to control an operation of the follicle separating unit.
