There are very few sex estimation methods specifically designed for or tested on Belgian skulls. The currently used methods for European populations have been developed using North American collections where individuals are categorized as White and/or having European ancestry. These frequently show discordance between the pelvic sex and cranial sex estimations highlighting the need for population specific methods. To fill this gap in our knowledge, several sex estimation methods, using 15 qualitative skull features, were tested on two Flemish (northern Belgium) skeletal collections; one archaeological (15th–17th century) and one forensic (20th century). The features were tested by themselves as well as in different combinations using logistic regression. The glabella is considered the best lone feature with a minimal accuracy of 78.4% and a sex bias of −5.2%. Furthermore, four sex estimation equations were developed for the skull, the cranium, the mandible, and the frontal bone separately. The skull has an accuracy of 89.3% and a bias of 0.8%. For the cranium, this is 87.5% and −0.3%, respectively, for the mandible 85.1% and −0.1%, and for the frontal bone it is 80.4% and −4.6%. The various tests confirm that many skull features can be used for sex estimation and can generate high sex estimation accuracy.