Background The association between dyslipidemia and atopic dermatitis in children is unclear. This study investigated the association between dyslipidemia and atopic dermatitis in children by analysis of disease onset, risk factors, and disease severity. Methods Subset I examined 7 year-old children in elementary school (n = 248) and Subset II was a retrospective long-term follow-up hospital based-study (n = 52,725) conducted from 1986 to 2016 that used propensity score matching. In the Subset I Study, total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), triglycerides (TG) were determined, and the severity of atopic dermatitis was determined using SCORing Atopic Dermatitis (SCORAD). In the Subset II Study, the time of atopic dermatitis onset was determined for asymptomatic subjects whose TC levels were below or above 170 mg/dL. Results Our Subset I Study indicated that children with atopic dermatitis (n = 69, 27.8%) had significantly higher levels of TC and TG, and that disease severity had significant associations with high levels of TC and TG, and a low level of HDL-C. Our Subset II Study (1,722 with high TC and 6,735 with normal TC after propensity score matching) indicated the high TC group had a greater hazard ratio (HR) for the onset of atopic dermatitis (consensus-based HR: 2.47; 95% CI: 1.23, 5.06, P = 0.012) during 5 years. Conclusion An abnormal blood lipid profile in children is associated with the presence and severity of atopic dermatitis. The risk of atopic dermatitis onset was significantly greater with high levels of TC.