Background Dyslipidemia contributes to the development of nephrolithiasis in adults; however its relationship to urolithiasis in children remains debatable, and will be clarified in the present work. Methods A case-control study was performed involving 58 pediatric patients diagnosed with upper urinary tract stones as well as 351 controls. Age, gender, body mass index (BMI), serum calcium, serum uric acid, blood glucose, blood lipids, and compositions of stones were compared. Results According to the univariate analysis, uric acid was higher (P < 0.01) but serum calcium lower in the stone group than the control (P < 0.05). As for the blood lipids, non-high-density lipoprotein cholesterol (non-HDL-c) was significantly higher in the stone group as compared to the control (P < 0.01), while total cholesterol, triglycerides, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol did not show statistical difference between the two groups. In the multivariate analysis, only non-HDL-c and serum uric acid were increased in the stone group (P = 0.003 andP = 0.008). In the stone compositions' analysis, serum uric acid and non-HDL-c were associated with percentage of uric acid and pure calcium oxalate stones, respectively. Conclusion Non-high-density lipoprotein cholesterol may act as a lipid risk factor for urolithiasis in children.