Objectives: This study aimed to investigate the impact of 3 isocaloric exercise programs on cardiac autonomic nervous system (ANS) functioning in children. Methods: One hundred nine children (39% boys and 61% girls) aged 10-13 years (mean 11.07 ± 0.81) were conveniently assigned to 1 of 4 groups as follows: Moderate-intensity continuous training (MICT; n = 29) at 65-70% of the predicted maximum heart rate (MHR), High-intensity interval training (HIIT; n = 29) at > 80% of the predicted MHR, HIIT and MICT combined on alternate weeks (ALT; n = 27), and a control group (n = 24). Morning ANS activity was assessed via analysis of heart rate variability (HRV), with the patient in supine position for 10 min, before and after the exercise intervention. Data Analysis: A 2-way analysis of variance was used to evaluate the effects of training on all HRV parameters (p < 0.05/4 = 0.0125). Results: After 5 weeks of training, significant improvements were observed for ln of the standard deviation of normal-to-normal intervals (p < 0.0001), ln of the root mean square of successive difference (p < 0.0001), and ln of standard deviation 1 (p < 0.0001), with superior results reported in the HIIT group (effect size [ES] = 2.22, 2.69, and 2.69) compared with the MICT (ES = 1.67, 1.75, and 1.75) and ALT (ES = 0.87, 1.06, and 1.06) groups, respectively. Conclusion: Short-term HIIT seems to induce superior alterations in cardiac ANS activity compared to MICT and ALT in children through enhanced vagal activity.