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The focus of this study is the implications of structural transformation for gender equality, specifically equal pay, in Sub-Saharan Africa. While structural transformation affects key development outcomes, including growth, poverty, and access to decent work, its effect on the gender pay gap is not clear ex-ante. This paper provides evidence on the extent and drivers of the gender pay gap in non-farm wage- and self-employment activities across three countries at different stages of structural transformation (Malawi, Nigeria and Tanzania). The analysis leverages nationally-representative survey data and decomposition methods, and is conducted separately among individuals residing in rural versus urban areas in each country. The results show that women earn 40 to 46 percent less than men in urban areas, which is substantially less than in high-income countries. The gender pay gap in rural areas ranges from (a statistically insignificant) 12 percent in Tanzania to 77 percent in Nigeria. In rural as well as urban areas, the gap is mostly explained by differences in workers’ characteristics, including education, occupation and sector. If men and women had similar characteristics, 74 percent of the rural gap and 76 percent of the urban gap would disappear. Our detailed decomposition results suggest that structural transformation does not consistently help bridge the gender pay gap. Gender-sensitive policies are required to ensure equal pay for men and women.