National efforts to reduce low birth weight (LBW) and child malnutrition and mortality prioritise economic growth. However, this may be ineffective, while rising gross domestic product (GDP) also imposes health costs, such as obesity and non-communicable disease. There is a need to identify other potential routes for improving child health. We investigated associations of the Gender Inequality Index (GII), a national marker of women's disadvantages in reproductive health, empowerment and labour market participation, with the prevalence of LBW, child malnutrition (stunting and wasting) and mortality under 5 years in 96 countries, adjusting for national GDP. The GII displaced GDP as a predictor of LBW, explaining 36% of the variance. Independent of GDP, the GII explained 10% of the variance in wasting and stunting and 41% of the variance in child mortality. Simulations indicated that reducing GII could lead to major reductions in LBW, child malnutrition and mortality in low- and middle-income countries. Independent of national wealth, reducing women's disempowerment relative to men may reduce LBW and promote child nutritional status and survival. Longitudinal studies are now needed to evaluate the impact of efforts to reduce societal gender inequality.