Objective: To compare the autonomic behavior between malnourished children and a control group using analysis of heart rate variability (HRV). Method: Data were analyzed from 70 children who were divided into two groups: malnourished and eutrophic, according to the Z‐score nutritional status for height and age. For analysis of HRV indices, heart rate was recorded beat to beat with the child in the supine position for 20 min. The analysis of these indices was performed using linear methods, analyzed in the time and frequency domains. Student's t‐test for unpaired data and the Mann–Whitney test were used to compare variables between groups, with a significance level of 5%. Results: A reduction in systolic and diastolic blood pressure and an increase in heart rate were found in malnourished children compared to eutrophic children. The HRV indices suggested that malnourished children present reductions in both sympathetic and parasympathetic autonomic nervous system activity. The SDNN, rMSSD, NN50, pNN50, SD1, SD2, TINN, LF (ms2), and HF (ms2) indices were lower in malnourished children. Conclusion: Malnourished children present changes in cardiac autonomic modulation, characterized by reductions in both sympathetic and parasympathetic activity, as well as increased heart rate and decreased blood pressure.