The use of bioelectrical impedance analysis (BIA) in clinical settings is common. However, the value of BIA-based parameters in diagnosing metabolic syndrome (MetS) in children is under-investigated. Herein, we aimed to study the usefulness of BIA-indices in the diagnoses of MetS in 6–10-year-old girls. Therefore, a diagnostic accuracy case-control study was conducted, which included 75 girls aged 10–16 years, divided into three age-matched groups (normal, None-MetS, and MetS). Anthropometric indices, BIA parameters (including fat-free mass (FFM), body fat percent (BFP), and total body water (TBW)), blood pressure (BP), and blood samples were collected. Our main findings show that for girls in None-MetS and MetS groups, the waist circumference (WC) correlated positively with waist-hip ratio and mid-arm circumference (r = 0.58, 0.47, respectively), but not with BFP based on skinfold thickness (SFT), or mid-arm muscle area. WC was positively correlated with FFM and TBW, while high-density lipoprotein was inversely correlated with FFM. However, fasting blood glucose, triglycerides and BP showed no association with anthropometric measurements and BIA components. WC was the best indicator of MetS (AUC = 0.88, cut-off = 81.5 cm), followed by BMI (AUC = 0.84, cut-off = 26.9 kg/m2), while BFP based on SFT was the least sensitive (62.5%). In conclusion, apart from the FM index, anthropometric parameters such as WC are more valuable in diagnosing MetS in young adolescent girls.