Leptin and adiponectin have effects on the regulation of appetite and body composition, but evidence of these relationships in children is still limited. Even though investigations of their role in children with ASD are incipient, the nutritional aspects and eating difficulties that these patients may present are increasingly highlighted, often leading to inadequate nutritional status. This cross-sectional controlled study investigated the levels of adipokines in ASD children in comparison with healthy controls, and their correlations with nutritional aspects and lipid profile. A total of 80 participants (40 ASD and 40 controls) were included and evaluated through anthropometric variables, body composition, and blood samples. ASD participants showed higher levels of leptin, no changes of adiponectin levels in comparison with typically developing children, and a positive correlation between leptin and fat mass. This novel finding supports the role of leptin as a marker of adiposity in ASD children, which is reiterated by the higher leptin/adiponectin ratio and its correlation with fat mass in patients. Inverse correlation of leptin with HDL-cholesterol could only in certain cases be related to the higher adiposity in patients when compared to controls. These results highlight also the importance of assessing the nutritional status of this population.