This study examined if the cranial measurements from Data Collection Procedures for Forensic Skeletal Material 2.0 are repeatable when measured in dry bones and MSCT images and if the virtual measurements correspond to the physical ones. The sample included 33 dry crania imaged by MSCT. Two observers measured dry bones, two placed landmarks on 2D and 3D MSCT reconstructions, and one conducted measurements/landmarking on both media. One of the observers for each media repeated the measurements. Technical and relative technical error of measurement (TEM and rTEM) and percentage differences were calculated to examine the repeatability of measurements and compare measuring modalities. Intraobserver rTEM was above 1.5% for six bone measurements: FOB, ZOB, OBB, NLH, DKB, MDH (1.51%–4.87%) and for seven MSCT measurements: OBH, FOB, OBB, MDH, NLB, ZOB, DKB (1.57%–5.55%). The interobserver rTEM was above the acceptable level (>2%) for 11 measurements: PAC, NLH, OBB, EKB, MAL, FOB, NLB, OBH, ZOB, DKB, and MDH (2.01%–9.34%). The percentage differences were not systematically larger for measurements taken by the same user on both modalities than those obtained by different users on the same modality. When physical and MSCT measurements were tested on sex classification standards, the proportion of crania classified as male or female did not significantly differ (P > 0.05). The study showed that physical and virtual cranial measurements could be interchangeable for developing or applying sex estimation standards. However, clarifications and adaptations are necessary for measurements of mastoid, nasal, and orbital regions that did not meet the standard criteria.