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Purpose To evaluate the differences in pediatric non-contrast low-dose head computed tomography (CT) between filtered-back projection and iterative model reconstruction using objective and subjective image quality evaluation. Methods A retrospective study evaluated children undergoing low-dose non-contrast head CT. All CT scans were reconstructed using both filtered-back projection and iterative model reconstruction. Objective image quality analysis was performed using contrast and signal-to-noise ratios for the supra- and infratentorial brain regions of identical regions of interest on the two reconstruction methods. Two experienced pediatric neuroradiologists evaluated subjective image quality, visibility of structures, and artifacts. Results We evaluated 233 low-dose brain CT scans of 148 pediatric patients. There was a ∼2-fold improvement in the contrast-to-noise ratio between gray and white matter in the infra- and supratentorial regions ( p < 0.001) using iterative model reconstruction compared to filtered-back projection. The white and gray matter signal-to-noise ratio improved more than 2-fold using iterative model reconstruction ( p < 0.001). Furthermore, radiologists graded anatomical details, gray-white matter differentiation, beam hardening artifacts, and image quality using iterative model reconstructions as superior to filtered-back projection reconstructions. Conclusion Iterative model reconstructions had better contrast-to-noise and signal-to-noise ratios with fewer artifacts in pediatric CT brain scans using low-dose radiation protocols. This image quality improvement was demonstrated in the supra- and infratentorial regions. This method thus comprises an important tool for reducing children’s exposure while maintaining diagnostic capability.