It has been suggested that upper-body fat compared with lower-body fat is more closely associated with cardiovascular abnormalities. Our objective was to analyze the relationship between central fat (CF) and cardiac autonomic (cANS) function in obese and overweight girls. Children were classified in two groups based on CF: those above (CFa(50)) and those below the 50th percentile (CFb(50)) of the entire sample. This study included 16 female children who were diagnosed as being overweight or obese (age: 14.3 ± 2.8 years; weight: 75.0 ± 15.8 kg; height: 157.1 ± 8.9 cm; body mass index: 30.1 ± 5.4; and total body fat: 40.5 ± 5.0%; Tanner stage: 4). cANS function was assessed through heart rate variability (HRV) and CF parameters by dual-energy X-ray absorptiometry. Female children with higher CF exhibited significantly higher sympathetic and lower parasympathetic modulation than those with lower CF, independently of total body fat. The data of the present study indicate that CF is associated with less favorable indexes of HRV. In addition, our findings suggest that CF might be an important measure to assess the effect of obesity on cANS function in female children.