Girls typically show much lower suicide rates than boys in most OECD countries. However, in South Korea, the suicide rate of girls almost reaches that of boys. Moreover, Korean girls’ suicide rate is remarkable even among other advanced countries. One potential approach to explaining Korean girls’ relatively high suicide rate is to investigate how their peer groups affect suicidal ideation, but this approach has rarely been explored in Korean adolescents. We tested how the gender heterogeneity of peer groups is associated with suicidal ideation by analyzing 2,990 adolescents from the 2018 Korean Children and Youth Well-Being Index Survey. For the analysis, logistic regression models with survey weights were used. The analysis revealed that adolescents with different-gender friends were associated with a higher likelihood of suicidal ideation than those with exclusively same-gender friends when adjusting for covariates. In addition, an analysis stratified by gender found that this association was significant only among girls. Furthermore, the protective power of having a mentor against suicidal ideation was significantly lower in girls with male and female friends than in girls with only female friends. The findings suggest a less protective role of different-gender peer groups for suicidal ideation among girls. During adolescent suicidality consultations, school counselors and practitioners should pay attention to the characteristics of adolescents’ peers, particularly their gender.