OBJECTIVES Physical inactivity is an important health concern worldwide. In this study, we examined the effects of an exercise intervention on children’s academic achievement, cognitive function, physical fitness, and other health-related outcomes. METHODS We conducted a population-based cluster randomized controlled trial among 2301 fourth-grade students from 10 of 11 public primary schools in 1 district of Ulaanbaatar between February and December 2018. Schools were allocated to an intervention or control group with 5 schools each by using urban and mixed residential area stratified block randomization. The intervention group received a 3-minute high-intensity interval exercise program that included jumps, squats, and various steps implemented twice weekly over 10 weeks for 10 to 25 minutes per session. The control group received the usual physical education class. The primary outcome was academic achievement assessed by scores on the national examination. A linear mixed-effects model was applied. The difference between preintervention and post intervention was compared by least-squares means, estimated on the basis of the interaction of group, measurement time point, and school location. Only 1 statistician, responsible for the analysis, was blinded. RESULTS Of 2301 students, 2101 (1069 intervention; 1032 control) were included in the analysis. Intervention group members in an urban area showed an 8.36-point improvement (95% confidence interval: 6.06 to 10.66) in academic scores when compared with the control group, whereas those in a mixed residential area showed a 9.55-point improvement (95% confidence interval: 6.58 to 12.51). No intervention-associated injuries were observed. CONCLUSIONS The exercise program significantly improved children’s academic achievement.