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Unlike previous literature that mainly examined the cognitive effects of single-sex education, this study investigates its effects on students’ mental health, focusing on depression, suicide-related behaviours, and the various causes of stress. Utilizing a national-level large-scale dataset of middle school students in South Korea and employing an instrument variable approach, we find that attending single-sex schools reduces the probability of depression in female students by about 9.9% points, while no significant effect is observed for male students. Additionally, our research regarding the causes of stress uncovers that single-sex schooling reduces the stress associated with peer relationships, particularly for girls. These findings imply that the non-cognitive benefits of single-sex education may be stronger than previously thought. As a result, we advocate for a more thoughtful and inclusive implementation of school policies, taking into consideration the impact of gender peer effects at school.