Background Vitamin D deficiency has been associated not only with cardiovascular disease itself but also with established cardiovascular risk factors, such as obesity, hypertension, dyslipidemia and hyperglycemia. Some studies report on the association between vitamin D and dyslipidemia among obese children. But it was thought to be natural that in obese children, low vitamin D level be associated with hyperlipidemia. So the objective of this study was to investigate the relationship between serum vitamin D level (25-hydroxyvitamin D, [25(OH)D]) and lipid profile in non-obese children. Methods The study was carried out from March to May 2017. 376 healthy volunteers, aged 9 to 18, were enrolled in our study. They underwent blood test necessarily including vitamin D, triglyceride (TG) and high density lipoprotein cholesterol (HDL-C). In this study, only non-obese children (BMI 23kg/m2) was 243. We divided subjects into two groups ; vitamin D deficiency ( 20ng/mL) or not. Student’s t-test and simple linear regression analysis were used to estimate the association between vitamin D and lipids. Results The mean of serum vitamin D level in 243 non-obese children was 17.27ng/mL. There was no difference to age or sex. And the mean of serum TG in same subjects was 85.54mmol/L. The levels of vitamin D were inversely associated with TG (β coefficient = -1.506, p 0.001) and TG/HDL-C (β coefficient = -0.041, p 0.001). The overall percentage of vitamin D less than 20ng/mL was 69.5%. In vitamin D deficient group had higher TG levels than vitamin D sufficient group (90.27 vs 74.74, p = 0.013). In addition, this tendency also appeared on TG/HDL-C (1.753 vs 1.358, p = 0.018). Conclusion It seems that vitamin D, itself influences lipid profile, even in non-obese children. Therefore, low vitamin D level might progress to dyslipidemia or obesity in non-obese children. To be sure, a longitudinal follow-up study would be required.