Background Chrononutrition may affect childhood cardiometabolic health. Understanding this relationship may be crucial for managing paediatric obesity. Objective To investigate the relationship between chrononutrition and cardiometabolic risk factors in prepubertal children. MethodsThis cross-sectional study included 93 participants (50 males, 5-12 years), categorized as healthy weight (HW, n = 34), overweight (OV, n = 10), obese (OB, n = 23) and severe obesity (SOB, n = 26). 24-h dietary recalls assessed participants' caloric and energy substrate intake, analysed for the morning (until 11 am), afternoon (11 am to 6 pm), night (after 6:01 pm), and total daily intake. Cardiometabolic risk was evaluated through fasting glycemia, insulinemia, HOMA-IR, total cholesterol (TC), HDL-cholesterol, LDL-cholesterol, triglycerides (TG), and ultrasound analysis of abdominal fat (AF) and carotid intima-media thickness (CIMT). Results OB and SOB subjects had significantly higher (p < 0.001) insulinemia, HOMA-IR, TG, and AF, compared to HW subjects. SOB subjects showed significantly higher (p < 0.05) total daily protein intake than HW subjects. Considering the total sample, morning carbohydrate intake was inversely associated (p < 0.05; r = -0.21) with TC. Afternoon total calories (r = -0.33), carbohydrate (r = -0.35), and lipid (r = -0.23) intake were inversely associated (p < 0.05) with insulinemia. Higher lipid intake was linked to lower HDL-cholesterol (r = -0.22), while protein intake was linked to higher BMI Z-Score (r = 0.25) and glycemia (r = 0.23). Nighttime protein intake was positively correlated (p < 0.05) with BMI Z-Score (r = 0.24), insulinemia (r = 0.24), HOMA-IR (r = 0.27), TG (r = 0.25), AF (r = 0.25), and CIMT (r = 0.27). Conclusion Higher morning and afternoon carbohydrate intake, increased afternoon caloric and lipid intake, and lower afternoon and night protein intake in prepubescents were associated with a better health profile, including improvements in cardiometabolic risk factors.