Introduction: Data from studies conducted to date have evaluated clinical atherosclerotic conditions in adult patients with atopic dermatitis (AD). Subclinical atherosclerotic changes that are a precursor of atherosclerotic conditions may begin in childhood. The aim of this study was to investigate the presence of subclinical atherosclerosis in pediatric patients with AD and to determine the associated risk factors. Methods: A total of 59 patients who were referred to our department over a 6-month period and diagnosed with AD, and 53 healthy controls with a similar age and gender were included in the study. Subclinical atherosclerosis markers (carotid intima media thickness [CIMT], distensibility, stiffness, and strain) were measured using conventional echocardiography. The patients’ age, SCORAD index, and duration of symptoms were recorded. Serum total immunoglobulin E, C-reactive protein (CRP), blood lipid profile, and complete blood count markers were measured. Results: The median age of the patients was 61 (10–103) months, and 59.3% of them were male. The patients with AD had a higher CIMT (1.60 ± 0.35 vs. 1.30 ± 0.50 mm) and a lower distensibility (0.006 ± 0.009 vs. 0.01 ± 0.008) and strain (0.10 ± 0.14 vs. 0.19 ± 0.14) than the healthy controls (p < 0.01 for all), but there was no significant difference with regard to stiffness (10.16 ± 21.75 vs. 8.99 ± 12.66). Significant correlations between CIMT and disease duration, age, and the SCORAD index were found (p < 0.01, p < 0.01, and p < 0.05, respectively). No correlation between the subclinical atherosclerosis markers and the other laboratory results was found (p > 0.05 for all). Conclusion: This study demonstrates that pediatric patients with AD may express subclinical atherosclerosis markers. The evaluation of subclinical atherosclerosis in these patients revealed that CIMT may be the most important marker, as it displayed positive correlations with symptom duration, age, and disease severity.