Background <p>Childhood obesity is a growing public health concern, associated with several systemic disorders including changes in retinal microvasculature. This study aims to assess the relationship between body composition, biochemical markers, and retinal microvascular changes in obese children.</p> Methods <p>In this cross-sectional study, 45 overweight and obese children and 46 age- and sex-matched healthy individuals were evaluated. In addition to physical examination, anthropometric measurements were obtained using a body composition analyzer. A comprehensive ophthalmic assessment was conducted for all participants, which included advanced optical biometry, autorefractometry, visual acuity testing, and slit-lamp examination. Retinal microvasculature was assessed using optical coherence tomography angiography (OCT-A). Biochemical markers, including lipid profile, liver function tests, and CRP (as marker of inflammation), were also analyzed.</p> Results <p>The mean ages were 10.18 and 9.40 years in the obese/overweight and normal weight groups, respectively. Increased foveal thickness (<i>p</i> = 0.04) and foveal vessel density (<i>p</i> = 0.01) in the superficial capillary plexus, and decreased vessel density in the inferior parafoveal region of the deep capillary plexus (<i>p</i> = 0.03) were observed in obese/overweight children. Adjusted and crude regression analysis showed significant associations between body mass index, percent body fat, fasting blood glucose, and serum alanine transaminase levels with foveal vessel density, as well as between body mass index and serum triglycerides levels with foveal thickness.</p> Conclusions <p>Our findings suggest that childhood obesity is associated with significant alterations in retinal microvasculature. We propose that retinal health assessments and biochemical evaluations be considered in the clinical management of obese children.</p>