Purpose: Preoperative three-dimensional computed tomography is currently the gold standard imaging modality in patients with craniofacial anomalies. In these patients, bone structural evaluation is paramount for surgical planning and evaluation of brain parenchyma is often secondary. With the significant complexity of these patients, a majority of patients undergo multiple Computed Tomography (CT) studies from infancy into adulthood. This study presents an ultra-low-dose CT protocol that limits the radiation exposure per CT scan in patients with craniofacial anomalies. Material and Methods: A total of 200 consecutive patients who underwent head CT for preoperative evaluation of craniofacial anomalies at Tertiary Children's Hospital were included in the study. The kVp, (KiloVoltage Peak) mA (milliAnperage), CT dose index (CTDI), and dose-length product (DLP) were documented from the dose page. Patients were stratified based on age for determining age specific effective dose and for age matched comparison. The age specific effective dose was derived by using the established conversion factor as described in the paper. (1) Standard t test was performed to determine the statistical significance of radiation dose reduction. The Institutional Review Board approved the study and data was collected from 2012–2014. Findings: Of the 200 patients assessed in our study, 90 patients had low-dose CT scans and 110 patients had ultra-low-dose CT scans of the head. All patients had diagnostic quality CT studies. The low-dose CT was performed at 120 kVp and 100 mA. The ultra-low-dose CT was performed at 80 kVp and fixed 80 mA. The minimum, maximum and mean effective dose before the introduction of the ultra-low-dose protocol was 0.8 mSv, 6.9 mSV and 2.82 mSv. The minimum, maximum and mean effective dose after the introduction of the ultra-low-dose protocol was 0.6 mSv, 3.8 mSV, and 1.37 mSv. The reduction in the effective radiation dose was statistically significant (standard t test; P = 0.0001). Conclusion: Compared to the regular low-dose protocol, the ultra-low-dose CT protocol provided appropriate diagnostic images with a significantly decreased radiation dose.