The present study examined the effect of aggression on peer acceptance among adolescents. We focused on the moderating effects of gender and participation in physical education activities and examined whether these effects varied during school transition. We used longitudinal data of adolescents aged 10 to 17 years that were obtained from a survey that was conducted by the National Youth Policy Institute. In only early adolescence, the interaction effect of gender and physical education activity influenced the relationship between aggression and peer acceptance. Specifically, the negative relationship between aggression and peer acceptance was strengthened among female students who participated in physical education activities as compared to female students who did not. This effect was not observed in male students. However, during transition from primary to secondary school, the negative effect of physical education activities did not exist. For middle-adolescents, for whom physical education activities increased more than previous years, the negative relationship between aggression and peer acceptance worsened. These influences were the same, regardless of gender. Thus, this study suggests that physical education activities improve the negative relationship between aggression and peer acceptance during school transition.