Obesity is linked to the increasing prevalence of metabolic syndrome (MetS), even among the pediatric population. Some inflammatory and cardioembolic indexes derived from routine laboratory tests have captivated the attention of the medical community. Objectives: The aim of our study was to evaluate whether these markers are effective in distinguishing varying degrees of obesity and MetS in children and adolescents. Methods: We conducted a retrospective study. A total of 71 children and adolescents, aged between 6 and 16, were included in the study. Among them, 5 were overweight, 35 had obesity, and 31 had severe obesity. According to the NCEP ATP III criteria, 32 individuals had Metabolic Syndrome (MetS), while 39 did not have MetS. Results: The MetS positive group had higher values of TG/HDL-C (p < 0.001), TC/HDL-C (p < 0.001), MHR (p = 0.015), LHR (p = 0.001), NHR (p = 0.001), atherogenic index of plasma (p < 0.001), and PHR (p < 0.001). ESR, NLR, PLR, and SII did not progressively increase with the number of MetS criteria. The ROC curve analysis demonstrated that markers such as TG/HDL-C, the atherogenic index of plasma, TC/HDL-C, LHR, NHR, and PHR were effective in identifying MetS in children and adolescents with obesity. Conclusions: In conclusion, we determined that some novel inflammatory and cardioembolic indexes are useful in assessing MetS and obesity in children and adolescents.