The study of artificially deformed crania is complicated by difficulties in analyzing curvilinear shapes without reliable reference points for measurement. Methods of geometric morphometrics (GM) help to solve this problem. We generated 3D-models of deformed crania (26 male and 19 female) from burials of different chronological periods of the Okunev archaeological culture (Verkhniy Askiz I, Uybat III and V, Uybat-Charkov, Itkol I and II), Southern Siberia (2600–1700 BC). Using the Landmark IDAV software, each model was transformed into a set of six traditional craniometric landmarks and 450 semi-landmarks regularly distributed over the entire surface of the braincase. For further processing with the Procrustes and principal component analysis, functions of several R-packages (Morpho, Geomorph, and Arothron) were employed. Crania from early Okunev burials were found to have a small deformed area around lambda, spanning the posterior parts of parietal bones and the upper part of the occipital squama. In crania from later Okunev burials, the deformation extends on the parietal area, causing the reduction of cranial height owing to a lesser curvature of the parietal segment. The lateral walls of the braincase, the frontal squama, and the lower part of the occipital squama in such crania are more convex.