Malawi has experienced slow and uneven progress in school progression and completion rates, thus there is need to rethink the approaches needed for reforming education systems. Mothers are more likely to invest in children’s nutrition and well-being and take primary responsibility for children’s education. However, the association between women’s economic empowerment and their offspring’s school progression rates is not systematically understood in Malawi, or elsewhere. We investigate how economic empowerment of mothers is associated with children’s progression through grades at appropriate ages. Using the 2016/17 Malawi Integrated Household Survey data, we show that women’s economic empowerment is positively associated with being on-time for grade, with a steeper slope for girls than boys, particularly at secondary school level. The stronger association for girls in secondary school, who otherwise typically experience a higher risk of dropping out of school than boys, implies higher education attainment, and probably lower teen pregnancies and early marriage. We conclude that investment in women’s economic empowerment can significantly enhance school progression and completion rates and can contribute to human capital development and poverty reduction in Malawi and elsewhere in sub-Saharan Africa.