The aim of the study was to analyze heart rate dynamics in obese children by functional entropic measures of Heart Rate Variability (HRV). HRV is a simple, reliable, cheap and non-invasive measure of autonomic impulses. We applied five technques based on entropy to assess the level of complexity. These were Shannon, Multiscale Tsallis and Multiscale Rényi entropies. Then, Approximate and Sample entropies. Ninety-four children of mixed gender aged eight to twelve years were divided into two equal groups (n=47) based on body mass index: obese and non-obese weight ranges. HRV was monitored in the dorsal decubitus position for 20 minutes. After Anderson-Darling and Ryan-Joiner tests of normality, the parametric test ANOVA1 was applied for the statistical analysis, with the level of significance set at (p<0.05); so the probability of a type I error was less than 5%. All types of functional entropies were significant at that level with the exception of Sample entropy. Furthermore, for all five measures the chaotic response increased when undergoing change from non-obese to obese. Regarding the application of Principal Component Analysis (PCA) the first two components represent 98.9% of total variance; a steep scree plot. The Multiscale Rényi (α=0.25), Shannon and Multiscale Tsallis (q=0.25) entropies performed simlarly regarding PCA and ANOVA1; whilst the Approximate and Sample entropies were also analogous with respect to these particular statisical tests. The Approximate entropy performed the most strongly with respect to p-value (p=0.0092) by ANOVA1 and PCA. With the exception of Sample entropy the entropic techniques described here were able to significantly quantify the increase in chaotic response when non-obese to obese children were assessed by the HRV.