According to the World Economic Forum, the occupational gender gap with men dominating well-remunerated STEM careers is a key factor in the gender pay gap. However, the problem of underrepresentation of women in STEM fields is mitigated or reversed in some Eastern European and Islamic countries. This disparity suggests that cultural factors are at play. Gender-segregated schooling, which is commonly practiced in Islamic countries, is often seen as a contributing factor. However, the issue of gender-segregated education sparks much controversy. Critics argue evidence is lacking, and segregation may foster sexism and hinder social skills. In New Zealand, there is a significant opportunity to conduct research on gender segregation, as approximately 14.43% of girls and 14.35% of boys attend single-gender schools for their secondary (high school) education. In contrast to the USA and Australia, where single-gender schooling is predominantly offered by private and/or Catholic schools, the majority of New Zealand gender-segregated schools are state schools. Utilising the TIMSS 2019 dataset, our analysis revealed that girls from low socio-economic backgrounds and boys from higher socio-economic backgrounds who attend single-gender schools exhibit significantly higher mathematics and science achievement scores compared to their counterparts in co-educational settings. This success is particularly striking for girls in low socio-economic settings. Given mixed international evidence, this suggests that there must be protective factors at single-gender New Zealand schools, positively influencing these students. We examine potential factors setting apart girls-only schools to provide an explanation of our results: (1) a mitigated influence of gender socialisation practices and stereotype threat and (2) explicit messaging aimed at challenging stereotypes and empowering girls to actively engage in STEM fields.