Overhead throwing can cause asymmetric physical characteristics induced by certain repeated asymmetric movements. Characterizing these physical properties could provide insights for health promotion, conditioning, and training planning. The status of asymmetric body composition and physical function in overhead throwing sports athletes remains unclear. The aim of this study was to investigate body composition asymmetries in experienced overhead throwing sports athletes. This study included 77 college students classified into three groups, overhead throw sports, non-overhead throw sports, and non-sports experience groups, based on past and current sports activities and years of experience. A body composition analyzer was used to measure body composition variables. The asymmetry in body composition variables between limbs was evaluated using the asymmetry index. Differences between groups were compared using one-way analysis of variance and post-hoc tests. The lean muscle mass asymmetry index of the arms in the overhead throw group was significantly higher than that in the other groups. The dominant arm lean muscle mass in the overhead throw group was significantly higher than that in the other groups. However, the non-dominant arm lean muscle mass in the overhead throw group was significantly higher than that in the non-sports experience group. Overhead throwing sports results in increased muscle mass in the dominant arm and produces asymmetry in muscle mass between the arms. This asymmetry may be induced by repeated and frequent asymmetrical motions. Our findings highlight the importance of characterizing the effect of sports activities on the athletes and may provide insights for conditioning regimens for them.