Background Associations of cardiometabolic risk factors with heart rate variability (HRV) in children are unclear. We examined associations of cardiometabolic risk score (CRS) and individual cardiometabolic risk factors with HRV variables in 6‐ to 8‐year‐olds. Methods The participants were a population‐based sample of 443 children participating in baseline measurements of the Physical Activity and Nutrition in Children trial. Cardiometabolic risk factors included waist circumference (WC), insulin, glucose, triglycerides, HDL cholesterol, systolic blood pressure (SBP), and diastolic blood pressure (DBP). CRS was calculated as WC + insulin + glucose + triglycerides − HDL cholesterol + the mean of SBP and DBP. HRV variables (SDNN, RMSSD, HF, LF, LF/HF, Mean RR) were measured using 5‐minute electrocardiography at rest and analyzed using the Kubios HRV software. In this cross‐sectional study, associations of CRS and individual cardiometabolic risk factors with HRV were investigated using linear regression analyses adjusted for sex and peak height velocity. Results CRS was negatively associated with RMSSD, HF, Mean RR (P value < .05) and positively with LF/HF (P value = .005). Insulin was negatively associated with SDNN, RMSSD, HF, LF, and Mean RR (P value < .05) and positively with LF/HF (P value = .008). SBP was negatively associated with SDNN, RMSSD, HF, LF, and Mean RR (P value < .05). DBP was negatively associated with SDNN, RMSSD, and Mean RR (P value < .05). WC, glucose, triglycerides, or HDL cholesterol were not associated with HRV variables. Conclusions Higher CRS, insulin, and blood pressure were associated with smaller HRV, mainly indicating lower parasympathetic activity, in young children. This knowledge may help improving the clinical management of metabolic syndrome and cardiovascular diseases since childhood.