A method and apparatus for anonymizing a three-dimensional medical image are provided. The apparatus determines a skin region of a three-dimensional medical image, generates a human mask based on a human tissue region of the three-dimensional medical image, the human tissue region including various organs, generates a skin expansion region in which the skin region of the three-dimensional medical image is expanded, generates an anonymization region obtained by removing a region corresponding to the human mask from the skin expansion region, and changes brightness values of voxels corresponding to the anonymization region in the three-dimensional medical image to a predefined value or an arbitrary value.