Hypertension, central obesity, hyperglycemia, and dyslipidemia are key risk factors for cardiovascular disease. However, the specific factors contributing to the development of unfavorable cardiometabolic characteristics in children with obesity are unknown. In this study, we investigated the cross-sectional relationships between cytokines, irisin, and fatty acid (FA) composition in plasma in school-age children with metabolically healthy and unhealthy obesity (MHO and MUO, respectively) of the same age and body mass index and waist circumference percentiles. We compared the data with that of children with normal weight (NW). We found that inflammatory cytokines and low irisin plasma concentrations are associated with obesity but not with cardiometabolic risk (CMR). Lipid profiles showed that children with MUO have a distinctive FA profile compared with children with MHO and NW, whereas children with MHO shared 88% of the FA profile with the NW group. Among all FAs, concentration of myristic acid (14 : 0), arachidic acid (20 : 0), and n-3 polyunsaturated FAs (PUFAs) was higher in children with MHO, whereas n-6 PUFAs such as arachidonic acid (20 : 4n6) had a significant contribution in defining MUO. These data suggest that the plasma FA profile is not only a central link to obesity but also may act as an indicator of CMR presence.