The present 3D Dataset contains the 3D models of the endocranial cast of two specimens of Indohyus indirae described in the article entitled “The endocranial cast of Indohyus (Artiodactyla, Raoellidae): the origin of the cetacean brain” (Orliac and Thewissen, 2021). They represent the cast of the main cavity of the braincase as well as associated intraosseous sinuses.