Background Efforts to reduce the radiation dose have continued steadily, with new reconstruction techniques. Recently, image denoising algorithms using artificial neural networks, termed deep learning reconstruction (DLR), have been applied to CT image reconstruction to overcome the drawbacks of iterative reconstruction (IR). The purpose of our study was to compare objective and subjective image quality of DLR and IR on pediatric abdomen and chest CT images.Methods This retrospective study included pediatric body CT images from February 2020 to October 2020, performed on 51 patients (34 boys and 17 girls; age 1–18 years). Non-contrast chest CT (n = 16), contrast-enhanced chest CT (n = 12), and contrast-enhanced abdomen CT (n = 23) images were included. Standard 50% adaptive statistical iterative reconstruction V (ASIR-V) images were compared to images with 100% ASIR-V and DLR at medium and high strengths. Attenuation, noise, contrast to noise ratio (CNR), and signal to noise (SNR) measurements were performed. Overall image quality, artifacts, and noise were subjectively assessed by two radiologists using a four-point scale (superior, average, suboptimal, and unacceptable). Quantitative and qualitative parameters were compared using repeated measures analysis of variance (ANOVA) with Bonferroni correction and Wilcoxon signed-rank tests.Results DLR had better CNR and SNR than 50% ASIR-V in both pediatric chest and abdomen CT images. When compared with 50% ASIR-V, high strength DLR was associated with noise reduction in non-contrast chest CT (33.0%), contrast-enhanced chest CT (39.6%), and contrast-enhanced abdomen CT (38.7%) with increases in CNR at 149.1%, 105.8% and 53.1% respectively. The subjective assessment of overall image quality and noise was also better on DLR images (p < 0.001). However, there was no significant difference in artifacts between reconstruction methods.Conclusion Compared with 50% ASIR-V, DLR improved pediatric body CT images with significant noise reduction. However, artifacts were not improved by DLR, regardless of strength.