Background: Previous studies have separately reported the effects of physical exercise and yoga in children, showing physical, cognitive and emotional benefits., Objectives: The present randomized controlled trial assessed the effects of yoga or physical exercise on physical fitness, cognitive performance, self-esteem, and teacher-rated behavior and performance, in school children., Methods: 98 school children between 8 to 13 years were randomized as yoga and physical exercise groups {n = 49 each; (yoga: 15 girls, group mean age 10.4 ± 1.2 years), (physical exercise: 23 girls, group mean age 10.5 ± 1.3 years)}. Both groups were blind assessed after allocation, using: (i) the Eurofit physical fitness test battery, (ii) Stroop color-word task for children, (iii) Battle's self-esteem inventory and (iv) the teachers' rating of the children's obedience, academic performance, attention, punctuality, and behavior with friends and teachers. After assessments the yoga group practiced yoga (breathing techniques, postures, guided relaxation and chanting), 45 minutes each day, 5 days a week. During this time the physical exercise group had jogging-in-place, rapid repetitive movements and relay races or games. Both groups were assessed at the end of 3 months. Data were analyzed with RM ANOVA and post-hoc tests were Bonferroni adjusted., Results: There was one significant difference between groups. This was in social self-esteem which was higher after physical exercise compared to yoga (p < 0.05). All the changes reported below are based on after-before comparisons, within each group. Both groups showed an increase in BMI, and number of sit-ups (p < 0.001). Balance worsened in the physical exercise group, while plate tapping improved in the yoga group (p < 0.001). In the Stroop task both groups showed improved color, word- and color-word naming (p < 0.01), while the physical exercise group showed higher interference scores. Total, general and parental self-esteem improved in the yoga group (p < 0.05)., Conclusion: Yoga and physical exercise are useful additions to the school routine, with physical exercise improving social self-esteem., Trial Registration: The study was registered in the Clinical Trials Registry of India (CTRI/2012/11/003112).