In this sociometric study, we aimed to investigate the social position of gender-referred children in a naturalistic environment. We used a peer nomination technique to examine their social position in the class and we specifically examined bullying and victimization of gender dysphoric children. A total of 28 children (14 boys and 14 girls), referred to a gender identity clinic, and their classmates (n = 495) were included (M age, 10.5 years). Results showed that the gender-referred children had a peer network of children of the opposite sex. Gender-referred boys had more nominations on peer acceptance from female classmates and less from male classmates as compared to other male classmates. Gender-referred girls were more accepted by male than by female classmates and these girls had significantly more male friends and less female friends. Male classmates rejected gender-referred boys more than other boys, whereas female classmates did not reject the gender-referred girls. For bullying and victimization, we did not find any significant differences between the gender-referred boys and their male classmates nor between the gender-referred girls and their female classmates. In sum, at elementary school age, the relationships of gender dysphoric children with opposite-sex children appeared to be better than with same-sex children. The social position of gender-referred boys was less favorable than that of gender-referred girls. However, the gender-referred children were not more often bullied than other children, despite their gender nonconforming behavior.