Using the theoretical framework of Bronfenbrenner’s ecological model of peer aggression, the aim of the present study was to examine if we could use the same predictors of peer aggression at schools for boys and girls. The research included 880 participants, elementary school students from the fifth to the eighth grade, who self-estimated aggressive behavior toward their peers, affective empathy, impulsivity, parental behavior, peer acceptance, a number of friends, exposure to media, school climate, perception of neighborhood dangerousness, and also nominated aggressive peers and gave data about the school achievement and a number of friends. The same number of their parents gave data about family SES, while 107 teachers estimated attendance of parents at the parent-teacher meetings and other school events. Multivariate multilevel modeling revealed different predictors of boys vs girls peer aggression. Selected predictors of ecological model better explained peer aggression in boys than in girls. The main differences were in individual characteristic and family microsystem, whereas more statistically significant predictors were for boys, while some distal predictors in an interaction with individual characteristics and family microsystem were important in the explanation of boys’ aggressive behavior. The overall results indicate that gender, as a biological category, had a strong influence on peer aggression. Psychological characteristics, as well as parental upbringing, better explained boys’ than girls’ aggressive behavior. These findings are very important for the school policy, which means that the intervention and prevention programs for peer aggression should differ depending on the child’s gender.