Childhood obesity represents a public concern worldwide. Evidence indicates that fruits and vegetables (FV) consumed as part of the daily diet reduce the global burden of obesity. Indeed, FV are rich in bioactive compounds, including carotenoids, which exert health benefits as very potent natural antioxidants. Here, we compared the anthropometric characteristics and the skin carotenoid content between two schoolchildren populations from Southern and Central Italy to evaluate their dietary habits. A sample of 121 and 124 schoolchildren from primary schools in Central and Southern Italy, respectively, was recruited. All participants underwent anthropometric measurements and assessment of the adherence to the Mediterranean Diet (MD) by the KIDMED questionnaire and the skin carotenoid score by Veggie Meter. The mean body mass index (BMI) was significantly lower in participants from Central Italy than in those from Southern Italy. A significantly higher percentage of overweight and obesity was found in the overall sample from Southern than in Central Italy. The adherence to the MD was in the average range for both populations, with no gender-related differences. The carotenoid score was higher and negatively correlated with BMI in the schoolchildren from Central Italy. In multiple regression analyses, skin carotenoids were positively associated with the consumption of fruit in the entire sample. This study suggests the importance of increasing FV intake, particularly in Southern Italy, as a strategy for preventingof obesity during the whole lifespan. Further studies are essential to better understand the influence of skin carotenoids on different variables and their potential role as indicators of health status in children.