Aim: Although short-term cardiometabolic complications are not usually expected in children with metabolically healthy obesity (MHO), subclinical vascular damage may still occur. This study aimed to evaluate Fibroblast Growth Factor 21 (FGF21) levels in children with obesity and their relationship with carotid intima-media thickness (CIMT) and other cardiometabolic risk factors. Methods: Children with obesity were defined based on their metabolic health status. Children meeting all of the following criteria were categorised as MHO: High-density lipoprotein (HDL) > 1.03 mmol/L, triglycerides (TG) <= 1.7 mmol/L, systolic and diastolic blood pressure <= 90th percentile for age and height, and fasting glucose < 5.6 mmol/L. Children who did not meet one or more criteria were defined as having metabolically unhealthy obesity (MUO). Anthropometric measurements, serum FGF21 levels, biochemical tests and CIMT assessments were performed. Results: The study was conducted between March and September 2024 with 64 obese and 32 healthy children aged 7-18 years. Children with MUO had the highest mean FGF21 levels. CIMT values were significantly higher in children with MUO compared with children with MHO and healthy controls, whilst no difference was observed between children with MHO and healthy controls. No significant correlation was found between FGF21 and CIMT. Conclusions: FGF21 levels were elevated in children with MUO compared with children with MHO and healthy controls. However, FGF21 does not appear to be a reliable biomarker. Further studies are required to clarify this relationship.