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Background Sub-Saharan Africa suffers from the highest maternal mortality ratio (MMR) in the world, with 542 deaths per 100,000 live births in 2017, relative to a global ratio of 211. Reducing gender inequities, increasing awareness regarding gender-based discrimination (GBD), and increasing the empowerment of women and girls have recently been recognized as prerequisites for improving maternal health. Previous studies have shown GBD to be related to gender health inequities. GBD results in low utilization of maternal health services and poorer quality of care. However, there is very limited research available on the relationship between GBD and maternal mortality in Sub-Saharan Africa (SSA). Methods We investigated the association between self-reported GBD and maternal mortality in an ecological study. We combined survey data from Demographic and Health Surveys (DHS) and from Afrobarometer across 78 sub-national regions, located in nine Sub-Saharan African countries. Data were analyzed using a random intercept two-level regression model, while controlling for relevant covariates at region- and country-level. Results The proportion of women who reported experiencing GBD varied between 0% in several regions in Benin, Mali, Senegal, South Africa, and Zimbabwe and 24·7% in Atacora, Benin. We identified a positive association between the proportion of women who reported experiencing GBD in a region in the past year and MMR. A 1% increase in the proportion of women experiencing GBD resulted in an increase of the MMR by nearly two, i.e., in two more maternal deaths per 100,000 live births. This association was even more pronounced after adjusting for region-level covariates, but did not change with the inclusion of country-level covariates. Conclusions Our findings show that the rate of self-reported GBD is associated with maternal mortality in a region, even after controlling for other factors that are known to influence maternal deaths. However, our model does not allow to rule out endogeneity. Further research is needed to unravel causal pathways between GBD and maternal mortality.