Background: This study aimed to compare the accuracy of linear measurements obtained using the classical (manual) method versus cone-beam computed tomography (CBCT) in craniofacial anthropometry, specifically targeting the infraorbital foramen (IOF). Methods: This study involved two sample groups: one of 40 dry skulls measured manually using digital calipers, and the other of 40 CBCT 3D images digitally measured. Measurements included IOF height, distances between the IOF and nasion (N), IOF and frontomalar orbital (FMO), and between the two IOFs. Statistical analysis was performed using an ANOVA, t-test, and Fisher’s test with a significance level of 0.05. Results: The manual method recorded a mean IOF height of 2.1 mm, while CBCT showed a mean of 3.52 mm. Significant differences were recorded between the two methods when measuring IOF height, with a p < 0.001. However, CBCT measurements generally yielded higher accuracy and lower variance due to the absence of significant differences (p > 0.05). The distance between the two IOFs measured by both methods differed significantly (p = 0.03157), with CBCT measurements showing higher values. Conclusions: In conclusion, although no significant differences were found in the overall accuracy of the two methods, CBCT proved to be a more reliable tool for detailed craniofacial measurements due to its higher accuracy and reproducibility. CBCT demonstrated superior consistency in measurements, offering enhanced precision in assessing craniofacial structures. These findings support the growing preference for CBCT in maxillofacial surgery, where precision is critical for successful outcomes. Nonetheless, manual techniques remain valuable in settings where advanced imaging is not accessible.