This study compared manual and digital measurements of plagiocephaly and brachycephaly in infants and evaluated whether three-dimensional (3D) digital photography measurements can be used as a superior alternative in everyday clinical practice. A total of 111 infants (103 with plagiocephalus and 8 with brachycephalus) were included in this study. Head circumference, length and width, bilateral diagonal head length, and bilateral distance from the glabella to the tragus were assessed by manual assessment (tape measure and anthropometric head calipers) and 3D photographs. Subsequently, the cranial index (CI) and cranial vault asymmetry index (CVAI) were calculated. Measured cranial parameters and CVAI were significantly more precise using 3D digital photography. Manually acquired cranial vault symmetry parameters were at least 5 mm lower than digital measurements. Differences in CI between the two measuring methods did not reach significance, whereas the calculated CVAI showed a 0.74-fold decrease using 3D digital photography and was highly significant (p < 0.001). Using the manual method, CVAI calculations overestimated asymmetry, and cranial vault symmetry parameters were measured too low, contributing to a misrepresentation of the actual anatomical situation. Considering consequential errors in therapy choices, we suggest implementing 3D photography as the primary tool for diagnosing deformational plagiocephaly and positional head deformations.