Lipoprotein a (Lp(a) is an independent risk factor for atherosclerotic cardiovascular disease. The prevalence of high Lipoprotein (a) (Lp(a)) in the Lebanese pediatric population is unknown. Our study aims to assess this prevalence and to study the relationship of Lp(a) with the lipid profile, age, body mass index (BMI) and socio-economic status (SES) in Lebanese schoolchildren. A total of 961 children aged 8–18 years (497 boys and 464 girls) were recruited from ten private and public schools in 2013–2014 using a stratified random sample. Schools were selected from the Greater Beirut and Mount Lebanon areas, and were categorized into three subgroups according to the schools’ SES status (high, medium, low). Lp(a) was assayed in 2018 on samples previously frozen at − 80 °C. Abnormal Lp(a) levels (≥ 75 nmol/L) were observed in 14.4% of the overall sample (13.5% for boys,15.3% of girls p = 0.56). The median of Lp(a) was 20(10–50) in the whole sample with no significant gender difference. No significant relationship was found between Lp(a) and age. However, Lp(a) was significantly correlated with BMI in whole sample, as well as in boys and girls (p = 0.02, p = 0.03, p = 0.03, respectively). A significant correlation was found between Lp(a) and non-HDL-C in the whole sample as well as in boys and girls (respectively p < 0.001,p = 0.024 and p = 0.03), but not with triglycerides and HDL-C. In a multivariate linear regression analysis, Lp(a) was only independently associated with BMI and non-HDL-C in boys and girls. Lp(a) was independently associated with BMI and non-HDL-C while no significant relationship was observed with age and sex confirming the strong genetic determination of Lp(a).