A phenotype of metabolically healthy obesity (MHO) has been described in youth with obesity, but data are still scarce in this age group. The aim of the current study was to describe and compare clinical and laboratory parameters related to obesity among three different groups of youth, namely youth with normal weight (NW), with MHO, and with metabolically unhealthy obesity (MUO). One hundred and three youngsters with obesity were divided according to 2018 consensus-based criteria into those with MHO [n = 49, age (±SD): 10.9 ± 2.9 years] and those with MUO [n = 54, 11.5 ± 2.7 years] and were compared to age-, sex- and Tanner-matched NW [n = 69, 11.3 ± 2.9 years]. Several obesity-related parameters were investigated for all three groups of children. Comparisons were made by analysis of variance (ANOVA) followed by the Fisher's PLSD test. Youth with MHO had lower systolic (p < 0.001) and diastolic (p < 0.01) blood pressure z-score and triglycerides (p < 0.01), but higher HDL-C (p < 0.001), total cholesterol (p < 0.05), and apo-A1 (p < 0.05) compared to those with MUO. Compared to controls, both children with MHO and MUO showed higher fasting insulin (p < 0.05), HOMA-IR (p < 0.05), and QUICKI (p < 0.001). Similarly, both groups had higher hsCRP, fibrinogen, uric acid, and leptin compared to controls (for all, p < 0.001), while their adiponectin was lower (p < 0.05). Visfatin was higher in children with MUO compared to controls (p < 0.01), and it showed a trend to be lower in children with MHO compared to those with MUO (p = 0.1). This study provides evidence that children identified as having MHO by the consensus-based criteria had better metabolic profiles than youth with MUO, but worse than NW. Further research is needed in pediatric populations both regarding MHO criteria and the nature of the MHO phenotype per se.