Introduction: The effectiveness of integrated approach using complementary therapies for children diagnosed with Autism spectrum Disorder (ASD) is poorly studied. This is due to limited objective assessments and lack of well-designed therapeutic module. Aim: This study examined the effect of yoga and naturopathy interventions on Electrophotonic Imaging (EPI) parameters in children with autism. Methods: This study consisted of three groups i.e., Yoga (YG), combination (Yoga and Naturopathy, YNG) and Control Group (CG) tested a 24 days intervention duration. Yoga group received series of yoga practices and combination groups received both yoga and naturopathy for the same duration. The control group maintained their daily usual activities. The EPI parameters included Activation Coefficient (AC, stress parameter), Integral Area (IA, general health parameter), Integral Entropy (IE, disorderliness parameter) were compared between groups and within group after interventions. Seventy-seven children with autism were randomized and 70 children completed the study with 95% adherence to the yoga and naturopathy interventions. Results: The results of the analysis showed that there was a significant improvement in energy level of YG and YNG in IAL (p<0.01; p<0.001), IEL (p<0.05; p<0.001) and no change in control group. Moreover, there were a significant difference in post assessment of YG and YNG from CG in IAL (p<0.001), IEL (p<0.05) and IAR (p<0.01) parameters of EPI. Conclusion: This study provides evidence that interventions of yoga and naturopathy may be useful to reduce the severity of symptoms and improve energy level that is required for children with autism and other neurodevelopmental disorders.