BACKGROUND: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impairment in social interactions, communication, restricted, and repetitive behaviors. Evidence-based treatment options for ASD are limited. Yoga is practiced by over 20 million people worldwide, and multiple studies have investigated yoga as a possible effective intervention for children with ASD. AIM: The aim of this study is to investigate the effect of yoga intervention on short-term heart rate variability (HRV) in children with ASD. METHODOLOGY: In this study, 50 children (38 boys and 12 girls) with ASD were recruited from Swabhimaan Trust, Palavakkam, Chennai. They were randomly grouped into ASD with yoga intervention group (n = 25) and ASD without yoga intervention group (n = 25) by simple lottery method. Yoga group children underwent yoga training for 3 months, and the control group did not receive any such training. For short-term HRV, 15 min electrocardiogram recording in sitting posture was recorded in lead II using a simple analog amplifier. RESULTS: In HRV, time domain parameters such as mean RR interval (0.72 [0.74] to 0.94 [0.92]), standard deviation of the NN intervals (52.04 [54.23] to 74.48 [72.80]), and root of the mean squared differences of successive NN interval (32.60 [34.40] to 40.83 [42.90]) significantly increased in ASD children after yoga intervention. In frequency-domain parameters, high frequency (HF) in n. u (48.08 [47.24] to 58.37 [59.22]) shows a significant increase and low frequency (LF) in n. u (52.4 [51.82] to 40.51 [40.12]), and LF/HF ratio (1.29 [1.31] to 0.78 [0.79]) shows a significant decrease in ASD with yoga intervention group children after 3 months of yoga training. CONCLUSION: Yoga interventions have been successful in bringing parasympathetic dominance in ASD children, and the greater advantage is being a noninvasive way of intervention to support children with ASD and help them to achieve physiological as well as psychological balance.