Background: Suicide ideation is a health issue affecting adolescents worldwide. There are significant variations in suicide ideation between countries and genders, which have not been fully explained. Research is especially lacking in countries outside Europe and North America. Gender equality has been shown to matter in other aspects of adolescent mental health, such as life satisfaction, but has not been researched in relation to suicide ideation at national level. Objective: To investigate how national gender inequality is related to self-reported suicide ideation among adolescents, and whether this association differs between boys and girls. Methods: This is a cross-national, cross-sectional study using individual survey data from the Global School-based Student Health Survey, a survey in Africa, Asia, Latin America and the South Pacific, developed and supported by among others the WHO and the CDC; connecting this to national data: the gender inequality index from the UNDP; controlling for GDP per capita and secondary school enrolment. The data was analysed using a multilevel logistic regression method and included 149,306 students from 37 countries. Results: Higher national gender inequality, as measured by the gender inequality index, was significantly associated with a higher likelihood of suicide ideation in both girls and boys (odds ratio: 1.38 p-value: 0.015), but for girls and both sexes this was only after adjusting for selection bias due to secondary school enrolment (as well as GDP/capita). Interaction models showed that this association was stronger in boys than in girls. Conclusions: National gender inequality seems to be associated with higher levels of suicide ideation among adolescents in mainly low-and middle-income countries, especially among boys.