Objective We aimed to study the prevalence of metabolic syndrome (MetS) and the factors associated with metabolic syndrome among obese children. Methodology We recruited 175 subjects, aged 7 to 18 years old, referred for obesity. We studied their demography (age, gender, ethnicity, family background), performed clinical/auxological examinations [weight, height, body mass index (BMI), waist circumference (WC), blood pressure (BP)], and analyzed their biochemical risks associated with metabolic syndrome [fasting plasma glucose (FPG), fasting lipid profile (FLP), fasting insulin, liver function tests (LFT)]. MetS was identified according to the criteria proposed by the International Diabetes Federation (IDF) for pediatric obesity. Multiple logistic regression models were used to examine the associations between risk variables and MetS. Results The prevalence of metabolic syndrome among children with obesity was 56% (95% CI: 48.6 to 63.4%), with a mean age of 11.3 ± 2.73 years. Multiple logistic regression analysis showed age [adjusted odds ratio (OR) 1.27, 95% CI: 1.15 to 1.45] and sedentary lifestyle (adjusted OR 3.57, 95% CI: 1.48 to 8.59) were the significant factors associated with metabolic syndrome among obese children. Conclusion The prevalence of metabolic syndrome among obese children referred to our centers was 56%. Older age group, male gender, birth weight, sedentary lifestyle, puberty and maternal history of gestational diabetes mellitus (GDM) were found to be associated with MetS. However, older age group and sedentary lifestyle were the only significant predictors for metabolic syndrome.