The purpose of this investigation was to examine cranial deformation versus normal cranial variation in ancient Korean populations from the 1st century B.C. to the 7th century A.D. by means of geometric morphometrics and multivariate statistical methods. The samples of human crania in this study were 7 male and 11 female individuals from the Yean-ri site, 4 males and 6 females from the Nukdo site, and 6 males and 4 females from the Imdang site. Of the 38 adult individuals, 2 females (Ye085 and Ye099) from the Yean-ri site were reported to have artificially deformed crania in a previous study. In the present study, two-dimensional geometric morphometric methodology was employed to evaluate cranial shape variation. Deformed crania were characterized as an anteroposterior modification based on Antón’s classification system. Deformed crania showed relatively flatter frontal and occipital bones and superoposteriorly developed parietal bones from a lateral view, which may reflect compensatory development due to pressure from an anterior to posterior direction. Moreover, Im095 (female) and Nu051 (male) had relatively flatter frontal bones and were similar to the deformed group; however, the convexity in the occipital bone was too pronounced to allocate these individuals to the deformed group.