The purpose of this study was to analyze the 12-week horse riding exercise effect on the locomotion of a body and bilateral balance and flexion/extension of trunk during the sit-to-stand(STS) in elementary and middle school students. One-hundred eleven participants were divided into three groups. Each group was subject to a different horse riding exercise: control group(n = 36), 1 time/week group(n=37), and 3 times/week group(n=38). Two-way repeated ANOVA was used to compare weight transfer time(WTT), trunk flexion velocity(TFV), trunk extension velocity(TEV), mean rising index(MRI), mean weight asymmetry( MWA) among the groups, and STS changes in before and after 12 weeks. There was a group interaction in WTT, TFV, TEV, MRI, and MWA with different responses to horse riding exercise participation. There was a significant increase in 1 time/week group and 3 times/week group of WTT, TFV, TEV, and MRI. Additionally, MWA(an index of a capacity for bilateral balance) in lower extremity was decreased in 3 times/week group. It seems that horse riding exercise positively affected musculoskeletal function of the trunk and lower extremity by accelerating locomotion and bilateral balance.