Purpose: Executive function, attention, and memory are an important indicator of cognitive health in children. In this study, we analyze the effect of yoga and physical exercise on executive functioning, attention, and memory. Methods: In this prospective two-armed randomized controlled trial, around 802 students from ten schools across four districts were randomized to receive daily 1 h yoga training (n = 411) or physical exercise (n = 391) for 2 months. Executive function, attention, and memory were studied using Trail Making Test (TMT). Yoga (n = 377) and physical exercise (n = 371) students contributed data to the analyses. The data were analyzed using intention-to-treat approach using Student's t-test. Results: There was a significant increase in numerical TMT (TMTN) values within yoga (t = −2.17; P < 0.03) and physical activity (PA) (t = −3.37; P < 0.001) groups following interventional period. However, there was no significant change in TMTN between yoga and PA groups (t = 0.44; P = 0.66). There was a significant increase in alphabetical TMT (TMTA) values within yoga (t = 6.21; P < 0.00) and PA groups (t = 1.19; P < 0.234) following interventional period. However, there was no significant change in TMTA between yoga and PA groups (t = 3.46; P = 0.001). Conclusion: The results suggest that yoga improves executive function, attention, and working memory as effectively as physical exercise intervention in adolescent schoolchildren.