Background Understanding the anatomy and morphological variability of the orbital region is of great importance in clinical practice, forensic medicine, and biological anthropology. Several methods are used to estimate sex based on the skeleton or parts of the skeleton: classic methods and the geometric morphometric method. The objective of this research was to analyse sex estimation of the orbital region on a sample of skulls from a Bosnian population using the geometric morphometric method. Materials and Methods The research was conducted on three-dimensional models of 211 human adult skulls (139 males and 72 females) from the Osteological Collection at the Faculty of Medicine in Sarajevo. The skulls were recorded using a laser scanner to obtain skull 3D models. We marked 12 landmarks on each model to analyse sexual dimorphism. Landmarks were marked using the program Landmark Editor. After marking the landmarks, we used the MorphoJ program to analyse the morphological variability between male and female orbital regions. Results After Procrustes superimposition, generating a covariant matrix, and introducing sex as a variable for classification, a discriminant functional analysis (DFA) was applied which determined the estimation for males with 86.33% accuracy and for females with 88.89% based on the form of the orbital region. The results of regression analysis showed that the size of the orbital region has a statistically significant effect on its shape's sexual dimorphism. After excluding the influence of size and providing DFA, we concluded that sex estimation was possible with 82.01% accuracy for males and 80.55% accuracy for females based on the shape of the orbital region in the examined sample. Conclusion Sex estimation based on the orbital region was possible with more than 80% accuracy for both sexes, which is a high percentage of correct estimation. Therefore, we recommend using the orbital region of the skull for sex estimation.